@STRING{ABC = {Adv.\ Biophys.\ Chem.}}
@STRING{ABJ = {A.\ Biophys.\ J.}}
@STRING{AC = {Acta~Cryst.}}
@STRING{ACA = {Acta~Cryst.~A}}
@STRING{ACB = {Acta~Cryst.~B}}
@STRING{ACD = {Acta~Cryst.~D}}
@STRING{ACIEE = {Angew.\ Chem.\ Int.\ Ed.\ Engl.}}
@STRING{ACMCS = {ACM Computing Surveys}}
@STRING{ACMTMS = {ACM Trans.\ Math.\ Softw.}}
@STRING{ACP = {Adv.\ Chem.\ Phys.}}
@STRING{ACR = {Acc.~Chem.~Res.}}
@STRING{ACS = {American Chemical Soc.}}
@STRING{AI = {Adv.\ Immunol.}}
@STRING{AIRS = {Adv.\ Infrared Raman Spectrosc.}}
@STRING{AJOP = {Am.\ J.\ Physiol.}}
@STRING{AJOPCP = {Am.\ J.\ Physiol.\ -- Cell Physiol.}}
@STRING{AJP = {Am.~J.~of Phys.}}
@STRING{AMC = {Appl.\ Math.\ Comput.}}
@STRING{AMS = {Am.\ Math.\ Soc.}}
@STRING{APB = {Arch.\ Phys.\ Biochem.}}
@STRING{APL = {Appl.\ Phys.\ Lett.}}
@STRING{APR = {Apr.}}
@STRING{APS = {American Physical Soc.}}
@STRING{ARB = {Ann.\ Rev.\ Biochem}}
@STRING{ARBB = {Ann.\ Rev.\ Biochem.\ Bioeng.}}
@STRING{ARBBC = {Ann.\ Rev.\ Biophys.\ Biophys.\ Chem.}}
@STRING{ARBBS = {Ann.\ Rev.\ Biophys.\ Biomol.\ Struct.}}
@STRING{ARBPB = {Ann.\ Rev.\ Biophys.\ Bioeng.}}
@STRING{ARCB = {Ann.\ Rev.\ Cell Biol.}}
@STRING{ARG = {Ann.\ Rev.\ Gen.}}
@STRING{ARM = {Ann.\ Rev.\ Med.}}
@STRING{ARP = {Ann.\ Rev.\ Phys.\ Chem.}}
@STRING{ARPC = {ARPC}}
@STRING{ARPT = {Ann.\ Rev.\ Pharm.\ Tox.}}
@STRING{AS = {Appl.\ Spectrosc.}}
@STRING{AUG = {Aug.}}
@STRING{BBA = {Biochim.\ Biophys.\ Acta}}
@STRING{BBAB = {Biochim.\ Biophys.\ Acta -- Bioenergetics}}
@STRING{BBG = {Ber.\ Bunsenges.\ Phys.\ Chem.}}
@STRING{BBRC = {Biochem.\ Biophys.\ Res.\ Commun.}}
@STRING{BC = {Biol.\ Cybernetics}}
@STRING{BCH = {Biochemistry}}
@STRING{BCHJ = {Biochem.\ J.}}
@STRING{BCHMBI = {Biochem.\ Mol.\ Biol.\ Intl.}}
@STRING{BCHS = {Biol.\ Chem.\ Hoppe-Seyler}}
@STRING{BIO = {Biophysics}}
@STRING{BJ = {Biophys.\ J.}}
@STRING{BM = {Biologicheskie Membrany}}
@STRING{BMB = {Bull.\ Math.\ Biol.}}
@STRING{BMN = {Biomembranes and Nutrition}}
@STRING{BP = {Biopolymers}}
@STRING{BPB = {Biol.\ Pharm.\ Bull.}}
@STRING{BPC = {Biophys.\ Chem.}}
@STRING{BR = {Biomedical Research}}
@STRING{BSM = {Biophys.\ Struct.\ Mechanism}}
@STRING{CACM = {Communications of the ACM}}
@STRING{CAS = {Colloids and Surfaces}}
@STRING{CB = {Curr.\ Biol.}}
@STRING{CBR = {Computers and Biomedical Research}}
@STRING{CDA = {Chemical Design Automation News}}
@STRING{CEE = {Computers and Elect.\ Engr.}}
@STRING{CEL = {Cell}}
@STRING{CELB = {Cell Biol.}}
@STRING{CHB = {Chem.\ Biol.}}
@STRING{CIP = {Computers in Physics}}
@STRING{CIR = {Circulation Research}}
@STRING{CJB = {Can.\ J.\ Biochem.}}
@STRING{CM = {Contemp.\ Math.}}
@STRING{COCB = {Curr.\ Opinion Cell.\ Biol.}}
@STRING{COCHB = {Curr.\ Opinion Chem.\ Biol.}}
@STRING{COSB = {Curr.\ Opin.\ Struct.\ Biol.}}
@STRING{CP = {Chem.\ Phys.}}
@STRING{CPC = {Comput.\ Phys.\ Commun.}}
@STRING{CPE = {Concurrency Pract.\ Exp.}}
@STRING{CPL = {Chem.\ Phys.\ Lett.}}
@STRING{CPLI = {Chem.\ Phys.\ Lipids}}
@STRING{CPR = {Comp.\ Phys.\ Rep.}}
@STRING{CR = {Chem.\ Rev.}}
@STRING{CS = {Chemica Scripta}}
@STRING{CSY = {Computing Systems}}
@STRING{CTB = {Comments Theoretical Biology}}
@STRING{CW = {Computerwoche}}
@STRING{DC = {Distributed Computing}}
@STRING{DEC = {Dec.}}
@STRING{DU = {Die Umschau}}
@STRING{EBJ = {Eur.\ Biophys.\ J.}}
@STRING{EJB = {Eur.\ J.\ Biochem.}}
@STRING{EJCN = {Eur.\ J.\ of Clin.\ Nutr.}}
@STRING{EMBO = {EMBO J.}}
@STRING{EPL = {Europhys.\ Lett.}}
@STRING{ER = {Endocrin.\ Rev.}}
@STRING{FASEB = {FASEB J.}}
@STRING{FEB = {Feb.}}
@STRING{FEBS = {FEBS Lett.}}
@STRING{FTRS = {Faraday Trans.\ Roy.\ Soc.}}
@STRING{GAD = {Genes and Development}}
@STRING{ICCSA = {Computational Science \& Its Applications}}
@STRING{IEEECC = {IEEE Concurrency.}}
@STRING{IEEECSE = {IEEE Comp.\ Sci.\ \& Eng.}}
@STRING{IEEEM = {IEEE Micro.}}
@STRING{IEEENN = {IEEE Trans.\ on Neural Networks}}
@STRING{IEEESMC = {IEEE Trans.\ on Systems, Man and Cybernetics}}
@STRING{IEEETPDS = {IEEE Trans.\ Paral.\ Distr.\ Syst.}}
@STRING{IEICECCS = {{IEICE} Trans.\ Fund.\ Electr.\ Comm.\ Comp.\ Sci.}}
@STRING{IJBB = {Indian J.\ Biochem.\ Biophys.}}
@STRING{IJC = {Israel Journal of Chemistry}}
@STRING{IJHPCA = {Int.\ J.\ of High Perf.\ Comp.\ App.}}
@STRING{IJMPC = {Int. J. of Modern Phys. C}}
@STRING{IJQC = {Int.\ J.\ Quantum Chem.}}
@STRING{IJQCS = {Int.\ J.\ Quantum Chem.\ Symp.}}
@STRING{IN = {Informatikberichte}}
@STRING{IRC = {Int.\ Rev.\ Cytol.}}
@STRING{IRPC = {Int.\ Rev.\ Phys.\ Chem.}}
@STRING{JAC = {J.\ Appl.\ Cryst.}}
@STRING{JACS = {J.\ Am.\ Chem.\ Soc.}}
@STRING{JAN = {Jan.}}
@STRING{JASA = {J.\ Am.\ Stat.\ Assoc.}}
@STRING{JB = {J.\ Biochem.}}
@STRING{JBB = {J.\ Bioenerg.\ Biomemb.}}
@STRING{JBC = {J.\ Biol.\ Chem.}}
@STRING{JBNMR = {J.\ Biomolecular NMR}}
@STRING{JBSD = {J.\ Biom.\ Struct.\ Dyn.}}
@STRING{JCAMD = {J.\ of Computer-Aided Molecular Design}}
@STRING{JCB = {J.\ Cell Biol.}}
@STRING{JCBC = {J.\ Cell.\ Biochem.}}
@STRING{JCC = {J.\ Comp.\ Chem.}}
@STRING{JCICS = {J. Chem. Inf. Comput. Sci.}}
@STRING{JCIS = {J.\ of Colloid and Interface Science}}
@STRING{JCMP = {J.\ Comput.\ Phys.}}
@STRING{JCN = {J.\ Comp.\ Neurol.}}
@STRING{JCP = {J.\ Chem.\ Phys.}}
@STRING{JCTC = {J. Chem. Theory Comput.}}
@STRING{JCS = {J.\ Chem.\ Soc.}}
@STRING{JFM = {J.\ Fluid Mech.}}
@STRING{JGP = {J.\ Gen.\ Physiol.}}
@STRING{JLMCS = {J.\ Lipid Mediators Cell Signalling}}
@STRING{JLR = {J.\ Lipid.\ Res.}}
@STRING{JLSR = {J.~Liposome Res.}}
@STRING{JMB = {J.\ Mol.\ Biol.}}
@STRING{JMC = {J.\ Med.\ Chem.}}
@STRING{JMEB = {J.\ Membr.\ Biol.}}
@STRING{JMG = {J.\ Mol.\ Graphics}}
@STRING{JMGM = {J.\ Mol.\ Graphics Mod.}}
@STRING{JML = {J.\ Mol.\ Liq.}}
@STRING{JMM = {J.\ Mol.\ Model.}}
@STRING{JMP = {J.\ Math.\ Phys.}}
@STRING{JMR = {J.\ Magn.\ Reson.}}
@STRING{JMRB = {J.\ Magn.\ Reson.\ Series B}}
@STRING{JMRCM = {J.\ Muscle Res.\ Cell Mot.}}
@STRING{JMS = {J.\ Mol.\ Struc.}}
@STRING{JN = {J.\ Neuroscience}}
@STRING{JOCS = {J.\ Cell Science.}}
@STRING{JOOP = {J.\ of Object-Oriented Programming}}
@STRING{JPA = {J.\ Phys.\ A}}
@STRING{JPC = {J.\ Phys.\ Chem.}}
@STRING{JPCA = {J.\ Phys.\ Chem.\ A}}
@STRING{JPCB = {J.\ Phys.\ Chem.\ B}}
@STRING{JPCP = {J.\ of Parallel Computation}}
@STRING{JPDC = {J.\ Paral.\ Distrib.\ Comp.}}
@STRING{JPF = {J.\ Phys.\ {I{}I} France}}
@STRING{JPOC = {J.\ Phys.\ Org.\ Chem.}}
@STRING{JPP = {J.\ Photochem.\ Photobiol.}}
@STRING{JPPB = {J.\ Photochem.\ Photobiol.\ B}}
@STRING{JPSJ = {J.\ Phys.\ Soc.\ Jpn.}}
@STRING{JSB = {J.\ Struct.\ Biol.}}
@STRING{JSBMB = {J.\ Steroid.\ Biochem.\ Molec.\ Biol.}}
@STRING{JSC = {J.\ Sol.\ Chem.}}
@STRING{JSCA = {Int.\ J.\ Supercomput.\ Appl.\ High Perform.\ Comput.}}
@STRING{JSP = {J.\ Stat.\ Phys.}}
@STRING{JTB = {J.\ Theor.\ Biol.}}
@STRING{JUL = {Jul.}}
@STRING{JUN = {Jun.}}
@STRING{LM = {Langmuir}}
@STRING{MA = {Macromolecules}}
@STRING{MAR = {Mar.}}
@STRING{MAY = {May}}
@STRING{MC = {mc}}
@STRING{MCB = {Mol.\ Cell.\ Biol.}}
@STRING{MCLC = {Mol.\ Cryst.\ Liq.\ Cryst.}}
@STRING{MCM = {MC-Mikrocomputerzeitschrift}}
@STRING{MCTS = {Makromolekulare Chemie Theory and Simulations}}
@STRING{ME = {Methods in Enzymology}}
@STRING{MEC = {Molecular Endocrinology}}
@STRING{MENG = {Molecular Engineering}}
@STRING{MM = {Microprocessing and Microprogramming}}
@STRING{MMS = {Multiscale Model. Simul.}}
@STRING{MP = {Mol.\ Phys.}}
@STRING{MRB = {MRS-Bulletin}}
@STRING{MRI = {Mag.\ Res.\ Imaging}}
@STRING{MRM = {Magn.\ Reson.\ Med.}}
@STRING{MRQ = {Mag.\ Res.\ Quarterly}}
@STRING{MS = {Molecular Simulation}}
@STRING{NAR = {Nucl.\ Acids Res.}}
@STRING{NASB = {{NATO} {ASI} Series~{B}}}
@STRING{NAT = {Nature}}
@STRING{NATNB = {Nature New Biol.}}
@STRING{NATOA = {{NATO} {ASI} Series~{A}: Life Sciences}}
@STRING{NATSB = {Nature Struct.\ Biol.}}
@STRING{NB = {New Biol.}}
@STRING{NC = {Neural Comp.}}
@STRING{NIPS = {NIPS-91}}
@STRING{NN = {Neural Networks for Computing}}
@STRING{NNET = {Neural Networks}}
@STRING{NOV = {Nov.}}
@STRING{OCT = {Oct.}}
@STRING{PA = {Parallel Computing}}
@STRING{PAC = {Pure Appl.\ Chem}}
@STRING{PC = {Phys.\ Chem.}}
@STRING{PCPB = {Photochem.\ Photobiol.}}
@STRING{PD = {Physica D}}
@STRING{PE = {Protein Engng}}
@STRING{PHCB = {Physical Biology}}
@STRING{PHOR = {Photosyn.\ Res.}}
@STRING{PHY = {Physica}}
@STRING{PHYA = {Physica A}}
@STRING{PHYB = {Physica B}}
@STRING{PHYS = {Physica Scripta}}
@STRING{PL = {Phys.\ Lett.}}
@STRING{PLA = {Phys.\ Lett. A}}
@STRING{PLB = {Phys.\ Lett. B}}
@STRING{PNAS = {Proc.\ Natl.\ Acad.\ Sci.\ USA}}
@STRING{PR = {Phys.\ Rev.}}
@STRING{PRA = {Phys.\ Rev.\ A}}
@STRING{PRB = {Phys.\ Rev.\ B}}
@STRING{PRD = {Phys.\ Rev.\ D}}
@STRING{PRE = {Phys.\ Rev.\ E}}
@STRING{PRL = {Phys. Rev. Lett.}}
@STRING{PRO = {PROTEINS:\ Struc.,\ Func.,\ and Genetics}}
@STRING{PROlong = {PROTEINS: Structure, Function, and Genetics}}
@STRING{PRSLA = {Proc.\ R.\ Soc.\ Lond.\ A.\ (Math.\ Phys.\ Sci.)}}
@STRING{PRSLB = {Proc.\ R.\ Soc.\ Lond.\ B.}}
@STRING{PS = {Protein Science}}
@STRING{PSFG = {PROTEINS:\ Struc.,\ Func.,\ and Genetics}}
@STRING{PTP = {Prog.\ Theoret.\ Phys.}}
@STRING{QCPEB = {Quantum Chemistry Program Exchange Bulletin}}
@STRING{QRB = {Quart.\ Rev.\ Biophys.}}
@STRING{RCB = {Rev.\ Can.\ Biol.}}
@STRING{RMP = {Rev.\ Mod.\ Phys.}}
@STRING{RPP = {Rep.\ Prog.\ Phys.}}
@STRING{SA = {Scient.\ Am.}}
@STRING{SCI = {Science}}
@STRING{SEP = {Sep.}}
@STRING{SIADS = {SIAM J.\ Appl.\ Dyn.\ Sys.}}
@STRING{SIN = {Seminars in Nephrology}}
@STRING{SJNA = {SIAM J. Numer.\ Anal.}}
@STRING{SJSC = {SIAM J.\ Sci.\ Comput.}}
@STRING{SJSSC = {SIAM J.\ Sci.\ Stat.\ Comput.}}
@STRING{SMRM = {Soc. of Magnetic Resonance in Medicine}}
@STRING{SPIE = {SPIE J.}}
@STRING{SSC = {Solid State Communications}}
@STRING{SSI = {Solid State Ionics}}
@STRING{SSRSD = {Sov.\ Sci.\ Rev.\ D.\ Physiochem.\ Biol.}}
@STRING{STR = {Structure}}
@STRING{STRB = {Struc.\ Bio.}}
@STRING{TCA = {Theoret.\ Chim.\ Acta}}
@STRING{TCB = {Trends in Cell Biology}}
@STRING{TCBB = {IEEE/ACM Trans.\ on Comp.\ Bio.\ and Bioinformatics}}
@STRING{TEM = {Trends Endocr.\ Metab.}}
@STRING{TIBS = {Trends Biochem.\ Sci.}}
@STRING{TINS = {TINS}}
@STRING{TSF = {Thin Solid Films}}
@STRING{UM = {Ultramicroscopy}}
@STRING{UNKNOWN = {Unknown source}}
@STRING{ZP = {Z.\ f.\ Physik}}
@STRING{ZPB = {Z.\ Physik B}}
@STRING{ZPC = {Z.\ Phys.\ Chem.}}

@ARTICLE{AsRe9x,
  author = {Uri M. Ascher and S. Reich},
  title = {The midpoint scheme and variants for {H}amiltonian systems: advantages
	and pitfalls},
  journal = SJSSC,
  note = {To appear}
}

@ARTICLE{BARS91,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten},
  title = {Exploiting Bi-Exponential Relaxation to Detect Capillaries in {MRI}},
  journal = MRM,
  note = {Submitted. [Beckman Institute Technical Report TB-91-23]},
  annote = {this publication has been replaced by BARS95},
  tbtechrep = {TB-91-23}
}

@ARTICLE{BEAS95,
  author = {R.C Beason and N. Dussourd and M.E. Deutschlander},
  title = {Behavioural evidence for the use of magnetic material in magnetoreception
	by a migratory bird},
  journal = {J.~Exp.~Biol.},
  volume = {198},
  pages = {141--146}
}

@INPROCEEDINGS{BEKK92A,
  author = {H. Bekker and H. J. C. Berendsen and E. J. Dijkstra and S. Achterop
	and Rudi van Drunen},
  title = {{GROMACS:} {A} Parallel Computer for Molecular Dynamics Simulations},
  booktitle = {Conference Proceeding Physics Computing},
  note = {submitted}
}

@INPROCEEDINGS{BEKK92B,
  author = {H. Bekker and H. J. C. Berendsen and E. J. Dijkstra and S. Achterop
	and Rudi van Drunen and D. v. d. Spoel and A. Sijbers and H. Keegstra
	and B. Reitsma and M. K. R. Renardus},
  title = {{GROMACS} Method of Virial Calculation Using a Single Sum},
  booktitle = {Conference Proceeding Physics Computing},
  note = {submitted}
}

@UNPUBLISHED{BENN00,
  author = {Ben-Nun, M and Mart{\'{\i}}nez, T J},
  title = {Direct Observation of Disrotatory Ring-Opening in Photoexcited Cyclobutene
	Using {\it Ab Initio} Molecular Dynamics},
  note = {In press},
  journal = JACS
}

@ARTICLE{BuPo9x,
  author = {V.~Buchholtz and T.~P{\"o}schel},
  title = {A Vectorized Algorithm for Molecular Dynamics},
  journal = {International Journal of Modern Physics C},
  nremark = {in skeel:~skeel/BN/MS/BuPo9x.tex}
}

@ARTICLE{COHE91,
  author = {J. M. Cohen and D. A. Micha},
  title = {Electronically Diabatic Atom-Atom Collisions. A Selfconsistent Eikonal
	Approximation},
  journal = {J. Chem. Phys},
  note = {submitted}
}

@UNPUBLISHED{ECEL,
  author = {E-Cell},
  title = {Institute for Advanced Biosciences: E-Cell Project},
  note = {\url{http://www.e-cell.org}}
}

@MISC{ELBE93,
  author = {R. Elber},
  title = {Personal communication}
}

@ARTICLE{EMER32,
  author = {R.~Emerson and A.~Arnold},
  title = {The photochemical reaction in photosynthesis},
  journal = {J.~Gen.~Physiol.},
  volume = {16},
  pages = {191--205}
}

@MISC{UpPExx,
  author = {Upsilon Pi Epsilon},
  title = {International Honor Society for the Computing Sciences},
  howpublished = {{\tt http://www.acm.org/upe/}}
}

@MISC{FOX,
  author = {FOX},
  title = {Software Maintenance - Fox Pro Wiki},
  note = {\url{http://fox.wikis.com/wc.dll?Wiki~SoftwareMaintenance~SoftwareEng}}
}

@UNPUBLISHED{FRIE91,
  author = {M. Friedrichs and R. Goldstein and P. G. Wolynes},
  title = {Generalized Protein Tertiary Structure Recognition using Associative
	Memory {Hamiltonian}s},
  note = {In press},
  journal = {J. Mol. Biol.}
}

@MISC{MPI194,
  author = {{MPI} {F}orum},
  title = {{MPI}: {M}essage-{P}assing {I}nterface},
  note = {{\small \texttt{http://www.mpi-forum.org/\-docs/\-docs.\-html}}}
}

@MISC{OPEN06,
  author = {Miron Livny},
  title = {Open {S}cience {G}rid},
  note = {{\small \texttt{http://www.opensciencegrid.org}}}
}

@MISC{TERA01,
  author = {Charlie Catlett},
  title = {TeraGrid},
  note = {{\small \texttt{http://www.teragrid.org}}}
}

@MISC{MPI297,
  author = {{MPI} {F}orum},
  title = {{MPI}-2: {E}xtensions to the {M}essage-{P}assing {I}nterface},
  note = {{\small \texttt{http://www.mpi-forum.org/\-docs/\-docs.\-html}}}
}

@ARTICLE{Sunxx,
  author = {Sun Geng},
  title = {Construction of high order symplectic RK methods},
  journal = {J. Comput. Math.},
  volume = {11},
  pages = {250--260},
  number = {3},
  nremark = {% RMcl: it looks quite % detailed as far as symplectic implicit RK
	goes.}
}

@BOOK{Goodxx,
  title = {Computer Modeling of Biomolecular Processes},
  author = {Goodfellow and Moss}
}

@ARTICLE{Grub9x,
  author = {Helmut Grubm{\"u}ller},
  title = {Predicting slow Structural Transitions in Macromolecular Systems:
	Conformational Flooding},
  journal = {Phys.\ Rev.\ E},
  note = {In press}
}

@INPROCEEDINGS{GrET9x,
  author = {H. Grubm{\"u}ller and N. Ehrenhofer and P. Tavan},
  title = {Conformational Dynamics of Proteins: Beyond the Nanosecond Time Scale},
  booktitle = {Proceedings of the Workshop `Nonlinear Excitations in Biomolecules',
	May 30--June 4, 1994},
  editor = {Michel Peyard},
  address = {Centre de Physique des Houches (France)},
  note = {In press}
}

@ARTICLE{Guns80,
  author = {W. F. van Gunsteren},
  title = {Constrained Dynamics of Flexible Molecules},
  journal = {Mol.\ Phys.},
  volume = {40},
  pages = {1015--1019}
}

@TECHREPORT{HEAT,
  author = {M. T. Heath and J. A. Etheridge},
  title = {ParaGraph: A tool for visualizing performance of parallel programs.},
  institution = {Oak Ridge National Laboratory}
}

@MISC{HYLC02,
  author = {J. Hermans and R.~H. Yun and J. Leech and D. Cavanaugh},
  title = {{SIGMA}: {SI}-mulations of {MA}-cromolecule},
  howpublished = {{\small \texttt{http://femto.med.unc.edu/SIGMA}}}
}

@ARTICLE{HESS97,
  author = {Ted Hesselroth and Klaus Schulten},
  title = {Receptive Field and Feature Map Formation in the Primary Visual Cortex
	via {Hebbian} Learning with Inhibitory Feedback},
  journal = NC,
  note = {Submitted.}
}

@ARTICLE{HESS97A,
  author = {Ted Hesselroth and Klaus Schulten},
  title = {The Dynamics of Image Processing by Feature Maps in the Primary Visual
	Cortex},
  journal = NC,
  note = {Submitted.}
}

@ARTICLE{HoLu98a,
  author = {Marlis Hochbruck and Christian Lubich},
  title = {A {G}autschi-Type Method for Oscillatory Second-Order Differential
	Equations},
  journal = {Numer.\ Math.},
  note = {To appear. Also SFB 382, Report Nr.\ 91, January 1998. Available
	via http://www.am.uni-duesseldorf.de/~marlis/marlispreprints.html}
}

@ARTICLE{HrRo9x,
  author = {Tomasz Hrycak and Vladimir Rokhlin},
  title = {An Improved Fast Multipole Algorithm for Potential Fields},
  journal = SJSC,
  note = {In press. {[Yale Univ.\ technical report YALEU/DCS/RR-1089}, November
	27, 1995]}
}

@MISC{IzagCar00,
  author = {J.~A. Izaguirre},
  title = {Efficient Multiscale MOLLY Integrators for Biomolecular Simulations},
  howpublished = {{\tt http://www.cse.nd.edu/~izaguirr/career/node6.html}}
}

@MISC{John9x,
  author = {S. C. Johnson},
  title = {Yacc: Yet Another Compiler-Compiler},
  howpublished = {\url{http://dinosaur.compilertools.net/yacc/index.html}},
  annote = {Online manual},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{LeSc9x,
  author = {M. E. Lesk and E. Schmidt},
  title = {Lex - A Lexical Analyzer Generator},
  howpublished = {\url{http://dinosaur.compilertools.net/lex/index.html}},
  annote = {Online manual},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{MART00,
  author = {R. C. Martin},
  title = {Design Principle and Design Patterns},
  note = {\url{ http://www.objectmentor.com}}
}

@ARTICLE{MOON93,
  author = {C. Moon and G.M. Preston and C.A. Griffin and E.W. Jab and P. Agre},
  title = {The human aquaporin-CHIP gene. Structure, organization, and chromosomal
	localization},
  journal = JBC,
  volume = {268},
  pages = {15772--8}
}

@ARTICLE{Moor65,
  author = {Gordon E. Moore},
  title = {Cramming more components onto integrated circuits},
  journal = {Electronics Magazine},
  volume = {38},
  number = {8},
  year = {1965},
  pages = {15772--8}
}

@MISC{NEUR,
  author = {NEURON},
  title = {NEURON website},
  note = {\url{http://www.neuron.yale.edu/neuron}}
}

@BOOK{Olivxx,
  title = {The Shaggy Steed of Physics},
  author = {D. Oliver},
  nremark = {SR: a very nice introduction to mechanical systems; It discusses the
	Kepler motion to great extent.}
}

@ARTICLE{OLSE91,
  author = {G. J. Olsen and R. Overbeek and N. Larsen and C. R. Woese},
  title = {The ribosomal {RNA} database project: Updated description},
  journal = {Nucleic Acids Res.},
  note = {In press}
}

@BOOK{Prud88I,
  title = {{Integrals and Series, Volume~1: Elementary Functions}},
  author = {Anatoli\u{\i} Platonovich Prudnikov and Y. A. Brychkov and O. I.
	Marichev}
}

@BOOK{Prud88II,
  title = {{Integrals and Series, Volume~2: Special Functions}},
  author = {Anatoli\u{\i} Platonovich Prudnikov and Y. A. Brychkov and O. I.
	Marichev}
}

@BOOK{Prud88III,
  title = {{Integrals and Series, Volume~3: More Special Functions}},
  author = {Anatoli\u{\i} Platonovich Prudnikov and Y. A. Brychkov and O. I.
	Marichev}
}

@ARTICLE{RoWe??,
  author = {Barry Robson and Paul Weiner et al},
  title = {Novel algorithms for searching conformation space.},
  nremark = {published 1994 or before}
}

@ARTICLE{ROTH92,
  author = {S. M. Roth and D. M. Schneider and L. A. Strobel and M. F. A. VanBerkum
	and A. R. Means and A. J. Wand},
  title = {Characterization of the Secondary Structure of Calmodulin Complex
	with a Calmodulin Binding Domain Peptide},
  journal = {Biochemistry},
  note = {In press}
}

@ARTICLE{Ryckxx,
  author = {Ryckaert, J.P.},
  title = {The Method of constraints: appication to a simple alkane model},
  journal = {computer Modelling of Fluids Polymers and Solids},
  pages = {189--201},
  editor = {Catlow, C. R. A. et al.}
}

@ARTICLE{SCHN92,
  author = {D. M. Schneider and M. J. Dellwo and A. J. Wand},
  title = {Fast Internal Dynamics of Human Ubiquitin},
  journal = {Biochemistry},
  note = {submitted}
}

@BOOK{SeRoxx,
  title = {Anatomy of the Canonical Transformation},
  author = {Sewell, M.J. and Roulstone, I.},
  series = {Scientific Paper No. 6},
  address = {Short Range Forecasting Division, Meteorological Office, UK.}
}

@ARTICLE{Smit?,
  author = {W. Smith},
  title = {Molecular dynamic on distributed memory (MIMD) parallel computers},
  journal = {Theoretica Chimica Acta},
  volume = {84},
  pages = {395},
  nremark = {W. Smith from Daresbury Laboratory in the UK. The title is "Molecular
	dynamic on distributed memory (MIMD) parallel computers". They have
	been doing this for a number of years, starting with a systolic loop
	program on transputers written in occam and are now working on a
	program using domain decomposition. They are even working on a parallel
	FFT algorithm for solving the long range electrostatics.}
}

@TECHREPORT{Sund,
  author = {Sridhar Sundaram},
  title = {Fast Algorithms for N-body Simulation},
  institution = {Cornell},
  nremark = {% in files i.e. ntb}
}

@MISC{FORT,
  author = {UNFP},
  title = {User Notes on Fortran Programming (UNFP): An Open Cooperative Practical
	Guide},
  note = {\url{http://www.ibiblio.org/pub/languages/fortran/unfp.html}}
}

@MISC{WGLB90,
  author = {M. S. Warren and T. C. Germann and P. S. Lomdahl and D.M . Beazley
	and J. K. Salmon},
  title = {Avalon: An {A}lpha/{L}inux Cluster Achieves 10 {GF}lops for \$150k}
}

@UNPUBLISHED{WiIzxx,
  author = {J.~J. Willcock and J.~A. Izaguirre},
  title = {SAMD 2: Object Oriented Program for Prototyping of Molecular Dynamics
	Programs},
  note = {to be submitted to {\em J.~Comp.~Phys.}}
}

@ARTICLE{WILT68,
  author = {W. Wiltschko},
  title = {\"{U}ber den Einflu\ss\ statischer {M}agnetfelder auf die {Z}ugorientierung
	der {R}otkehlchen (\em {E}rithacus rubecula)}
}

@MISC{WOLF01,
  author = {Bill Wolfer},
  title = {CSE 432: Software Engineering},
  howpublished = {Course Taught At The University Of Notre Dame, Fall 2001 }
}

@ARTICLE{YE--94,
  author = {Gordon Ye and Klaus Schulten},
  title = {Magnetic Sensory Mechanisms in Birds and Other Animals},
  note = {In Preparation.}
}

@MANUAL{ZERNXX,
  title = {ZINDO, A General Semi-Empirical Program Package},
  author = {Michael C. Zerner},
  organization = {Department of Biochemistry, University of Florida}
}

@ARTICLE{ZIMA93,
  author = {L. Zim\'{a}nyi and J. K. Lanyi},
  title = {Deriving the Intermediate, Spectra and Photocycle Kinetics from Time-Resolved
	Difference Spectra of Bacteriorhodopsin. The Simpler Case of the
	Recombinant {D96N} Proteins},
  journal = BCH,
  note = {submitted}
}

@MISC{MATH05a,
  author = {MATHML},
  title = {Math{M}{L} Home},
  howpublished = {\url{http://www.w3.org/Math}},
  year = {website},
  annote = {W3C Math Home},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{OGLE,
  author = {OGLE},
  title = {Ogle Large-Scale Scientific Data Visualizer},
  year = {website},
  note = {\url{http://www.cora.nwra.com/Ogle}}
}

@ARTICLE{Narumi,
  author = {T. Narumi and R. Susukita and T. Ebisuzaki and G. McNivern and B.
	Elmegreen},
  title = {Molecular Dynamics Machine: Special-Purpose Computer for Molecular
	Dynamics Simulations},
  journal = {Molecular Simulation},
  year = {Vol. 21, 1999}
}

@ARTICLE{SHU89,
  author = {W. W. Shu and L. V. Kal{\'e}},
  title = {A Dynamic Load Balancing Strategy for the Chare Kernel System},
  journal = {Proceedings of Supercomputing~'89},
  year = {November 1989},
  pages = {389--398}
}

@ARTICLE{Rich,
  author = {Rich Murphy},
  title = {Design Parameters for Distributed PIM Memory Systems},
  journal = {Masters Thesis, University of Notre Dame},
  year = {MAY 2000}
}

@UNPUBLISHED{Reic95a,
  author = {S. Reich},
  title = {On Higher-order Semi-explicit Symplectic Partitioned {R}unge-{K}utta
	Methods for Constrained {H}amiltonian Systems},
  note = {Preprint},
  year = {May 2, 1995},
  nremark = {mailed 95 may 3}
}

@ARTICLE{SCHI91D,
  author = {J. L. Schiano, A. G. Webb and R. L. Magin},
  title = {Feedback control of the nuclear magnetization state: experimental
	results},
  journal = {IEEE Trans. Med. Imaging},
  year = {In press}
}

@TECHREPORT{Bran95,
  author = {Achi Brandt},
  title = {Multiscale Research in Molecular Mechanics},
  institution = {Weizmann Inst. of Science},
  year = {April 1995},
  number = {WI/GC-3}
}

@BOOK{SpVexx,
  title = {Cell-to-Cell Mapping},
  publisher = {Springer-Verlag},
  year = {??},
  author = {???},
  address = {New York}
}

@ARTICLE{BSVI07,
  author = {Paul Brenner and Chris R. Sweet and Dustin VonHandorf and Jes\'{u}s
	A.\ Izaguirre},
  title = {Accelerating the Replica Exchange Method Through an Efficient All-Pairs
	Exchange},
  journal = jcp,
  year = {2007},
  volume = {126},
  pages = {074103},
  month = {February}
}

@INPROCEEDINGS{BWTS07,
  author = {P. Brenner and J. M. Wozniak and D. Thain and A. Striegel and J.
	W. Peng and J. A. Izaguirre},
  title = {Biomolecular {P}ath {S}ampling {E}nabled by {P}rocessing in {N}etwork 
	{S}torage},
  booktitle = {2007 IEEE International Parallel and Distributed Processing Symposium},
  year = {2007},
  pages={256}
}

@INPROCEEDINGS{CiSI07,
  author = {Trevor Cickovski and Chris Sweet and Jes\'{u}s A.\ Izaguirre},
  title = {{MDL,} {A} Domain-Specific Language for Molecular Dynamics},
  booktitle = {Proc. 40th Annual Simulation Symposium},
  year = {2007}
}

@ARTICLE{Huan07,
  author = {Chengbang Huang and Faruck Morcos and Simon P.\ Kanaan and Stefan
	Wuchty and Danny Z.\ Chen and Jes\'{u}s A.\ Izaguirre},
  title = {Predicting Protein-Protein Interactions from Protein Domains Using
	a Set Cover Approach},
  journal = TCBB,
  year = {2007},
  volume = {4},
  issue = {1},
  month = {Jan.},
  pages = {78--87},
}

@INPROCEEDINGS{SMCI07,
  author = {Marcin Sikora and Faruck Morcos and Daniel J. Costello Jr. and Jes\'{u}s
	A.\ Izaguirre},
  title = {Bayesian Inference of Protein and Domain Interactions Using the Sum-Product
	Algorithm},
  booktitle = {Proc. 2007 Information Theory and Applications Workshop},
  year = {2007}
}

@ARTICLE{Wozn08,
  author = {J. M.\ Wozniak and P. Brenner and D. Thain and A. Striegel and J.
	A.\ Izaguirre},
  title = {Making the Best of a Bad Situation: Prioritized Storage Management
	in GEMS},
  journal = {Future Generation Computer Systems},
  volume = {24},
  issue = {1},
  pages = {10--16},
  month = {Jan.},
  year = {2008},
}

@INPROCEEDINGS{AkRe06,
  author = {E. Akhmatskaya and Sebastian Reich},
  title = {The Targeted Shadowing Hybrid {M}onte {C}arlo ({TSHMC}) Method},
  booktitle = {New Algorithms for Macromolecular Simulation},
  year = {2006},
  editor = {Benedict Leimkuhler and Christophe Chipot and Ron Elber and Aatto
	Laaksonen and Alan Mark and Tamar Schlick and Christoph Sch\"utte
	and Robert Skeel},
  volume = {49},
  series = {{LNCS}},
  pages = {141--151},
  address = {Secaucus, NJ, USA},
  publisher = {Springer-Verlag New York}
}

@ARTICLE{Akke06,
  author = {R.~L.~C.~Akkermans},
  title = {The {L}angevin {E}quation for {G}eneralized {C}oordinates},
  journal = {New Algorithms for Macromolecular Simulation. Lecture Notes in Computational
	Science and Engineering (LNCS). Springer Verlag. New York and Berlin.(page
	155-165)},
  year = {2006},
  volume = {49}
}

@ARTICLE{Dee+06,
  author = {S. Deechongkit and H. Nguyen and M. Jager and E. T. Powers and M.
	Gruebele and J. W. Kelly},
  title = {Beta-Sheet Folding Mechanisms from Perturbation Energetics},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2006},
  volume = {16},
  pages = {94--101}
}

@ARTICLE{DPGT98,
  author = {R. Du and V. S. Pande and A. Y. Grosberg and T. Tanaka and E. Shakhnovich},
  title = {On the transition coordinate for protein folding},
  journal = JCP,
  year = {1998},
  volume = {108},
  pages = {334}
}


@MASTERSTHESIS{Hamp05,
  author  = {Scott S. Hampton},
  title   = {Improved sampling of configuration space of biomolecules using shadow hybrid {M}onte
             {C}arlo},
  school  = {University of Notre Dame},
  year    = {2005},
  address = {Notre Dame, Indiana, USA}
}

@PHDTHESIS{Hamp07,
  author  = {Scott S. Hampton},
  title   = {Analysis of shadow hybrid {M}onte {C}arlo methods},
  school  = {University of Notre Dame},
  year    = {2007},
  address = {Notre Dame, Indiana}
}

@INPROCEEDINGS{Hamp06,
  author = {Scott S. Hampton and Paul Brenner and Aaron Wenger and Santanu Chatterjee
	and Jes\'us A. Izaguirre},
  title = {Biomolecular Sampling: {A}lgorithms, Test Molecules, and Metrics},
  booktitle = {New Algorithms for Macromolecular Simulation},
  year = {2006},
  editor = {Benedict Leimkuhler and Christophe Chipot and Ron Elber and Aatto
	Laaksonen and Alan Mark and Tamar Schlick and Christoph Sch\"utte
	and Robert Skeel},
  volume = {49},
  series = {{LNCS}},
  pages = {103--121},
  address = {Secaucus, NJ, USA},
  publisher = {Springer-Verlag New York}
}

@ARTICLE{HuiS06,
  author = {W.~Huisinga and B.~Schmidt},
  title = {Metastability and {D}ominant {E}igenvalues of {T}ransfer {O}perators},
  journal = {New Algorithms for Macromolecular Simulation. Lecture Notes in Computational
	Science and Engineering (LNCS). Springer Verlag. New York and Berlin.
	(page 167-182)},
  year = {2006},
  volume = {49}
}

@ARTICLE{Koeh06,
  author = {P. Koehl},
  title = {Electrostatics Calculations: Latest Methodological Advances},
  journal = cosb,
  year = {2006},
  volume = {16},
  pages = {142--151}
}

@ARTICLE{MBG+0x,
  author = {Roeland M. H. Merks and Sergey V. Brodsky and Michael S. Goligorsky
	and Stuart A. Newman and James A. Glazier},
  title = {Cell elongation is key to {\em in silico} replication of {\em in
	vitro} vasculogenesis and subsequent remodeling},
  journal = {Dev. Biol.},
  year = {2006},
  volume = {289},
  pages = {44--54},
  number = {1}
}

@ARTICLE{MHK+06,
  author = {R. M. H. Merks and A. G. Hoekstra and J. A. Kaandorp and P. M. A.
	Sloot and P. Hogeweg},
  title = {Problem-Solving Environments for Biological Morphogenesis},
  journal = {Computing in Science and Engineering},
  year = {2006},
  volume = {8},
  pages = {61--72}
}

@INPROCEEDINGS{Morc06,
  author = {Faruck Morcos and Mike Boxem and Niels Klitgord and Marc Vidal and
	Jes\'{u}s A.\ Izaguirre},
  title = {Prediction of domain interactions in {C}. elegans},
  booktitle = {Proc. Workshop Computational Biophysics to Systems Biology CBSB06},
  year = {2006}
}

@ARTICLE{PePa06,
  author = {P.~Petrone and V.~Pande},
  title = {Can Conformational Change be described by only a few normal modes?},
  journal = BJ,
  year = {2006},
  volume = {90},
  pages = {1583-1593}
}

@UNPUBLISHED{SHIS07,
  author = {Chris R. Sweet and Scott S. Hampton and Jes\'us A. Izaguirre and Robert D. Skeel},
  title  = {Separable shadow hybrid {M}onte {C}arlo method},
  note   = {In preparation},
  year   = {2007}
}

@TECHREPORT{SwHI06,
  author      = {Chris R. Sweet and Scott S. Hampton and Jes\'us A. Izaguirre},
  title       = {Optimal implementation of the Shadow Hybrid {M}onte {C}arlo method},
  institution = {Univ.~of Notre Dame},
  year        = {2006},
  number      = {TR-2006-09}
}

@UNPUBLISHED{SwHI07,
  author = {Chris R. Sweet and Scott S. Hampton and Jes\'us A. Izaguirre},
  title  = {Optimal implementation of the Shadow Hybrid {M}onte {C}arlo method},
  note   = {In preparation},
  year   = {2007}
}

@INPROCEEDINGS{SwIz06,
  author = {Chris R. Sweet and Jes\'us A. Izaguirre},
  title = {Backward error analysis of multiscale symplectic integrators and
	propagators},
  booktitle = {Proc. Third International Conference Multiscale Materials Modeling
	MMM2006},
  year = {2006}
}

@ARTICLE{TrTH06,
  author = {Simon Trebst and Matthias Troyer and Ulrich H. E. Hansmann},
  title = {Optimized parallel tempering simulations of proteins},
  journal = JCP,
  year = {2006},
  volume = {124},
  pages = {174903}
}

@ARTICLE{Vote06,
  author = {A. F. Voter},
  title = {Introduction to the Kinetic Monte Carlo Method},
  journal = {Proceedings of the NATO Advanced Study Institute on Radiation Effects
	in Solids, Edited by Kurt E. Sickafus, Eugene A. Kotomin, and Blas
	P. Uberuaga},
  year = {2006},
  volume = {235},
  pages = {1}
}

@ARTICLE{WaCJ06,
  author = {D.~J.~Wales and J.~M.~Carr and T.~Jones},
  title = {Overcoming Energetic and Time Scale Barriers Using the Potential
	Energy Surface},
  journal = {New Algorithms for Macromolecular Simulation. Lecture Notes in Computational
	Science and Engineering (LNCS). Springer Verlag. New York and Berlin.
	(page 73-87)},
  year = {2006},
  volume = {49}
}

@MISC{wiki:cumulant,
  author = {Wikipedia},
  title = {Cumulant --- Wikipedia{,} The Free Encyclopedia},
  year = {2006},
  note = {[Online; accessed 12-October-2006]},
  url = {\url{http://en.wikipedia.org/w/index.php?title=Cumulant&oldid=77687148}}
}

@INPROCEEDINGS{Wozn06,
  author = {Justin Wozniak and Paul Brenner and Doug Thain and Aaron Striegel
	and Jes\'{u}s A.\ Izaguirre},
  title = {Applying feedback control to a replica management system},
  booktitle = {Proc. of 38th Southeastern Symposium on System Theory},
  year = {2006}
}

@INPROCEEDINGS{Thai05b,
  author = {D. Thain and S. Klous and J. Wozniak and P. Brenner and A. Striegel
	and J. A. Izaguirre},
  title = {Separating Abstractions from Resources in a Tactical Storage System},
  booktitle = {Proceedings of Supercomputing 2005},
  year = {2005},
  address = {Seattle, WA},
  month = {Nov.}
}

@TECHREPORT{YaCI05,
  author = {C. B. B. Yau and T. Cickovski and J. A. Izaguirre},
  title = {{M}olecular {D}ynamics {L}anguage ({M}{D}{L})},
  institution = {University of Notre Dame},
  year = {2005},
  number = {13},
  address = {Department of Computer Science and Engineering},
  month = AUG
}

@TECHREPORT{Aras05,
  author = {K. Aras and T. Cickovski and D. Cieslak and C. Huang and J. A. Izaguirre},
  title = {Simulation of Chicken Limb Growth With Irregular Domain Shape},
  institution = {University of Notre Dame},
  year = {2005},
  number = {9},
  address = {Department of Computer Science and Engineering},
  month = JUL
}

@TECHREPORT{BrCI05,
  author = {D. Brandtner and T. Cickovski and J. A. Izaguirre},
  title = {Interactive Molecular Dynamics},
  institution = {University of Notre Dame},
  year = {2005},
  number = {11},
  address = {Department of Computer Science and Engineering},
  month = JUL
}

@MISC{YASA05,
  author = {YASARA},
  title = {Yet Another Scientific Artificial Reality Application},
  howpublished = {\url{http://www.yasara.com/index.html}},
  month = JUN,
  year = {2005},
  annote = {YASARA home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{PHP05,
  author = {PHP},
  title = {PHP: Hypertest Preprocessor},
  howpublished = {\url{http://www.php.net}},
  month = APR,
  year = {2005},
  annote = {PHP home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{LaTe05,
  author = {LaTeX},
  title = {A document preparation system},
  howpublished = {\url{http://www.latex-project.org}},
  month = FEB,
  year = {2005},
  readme = {Requires \usepackage{url} in the preamble.}
}

@TECHREPORT{THAI05,
  author = {D. Thain},
  title = {An architecture for cooperative storage},
  institution = {University of Notre Dame},
  year = {2005},
  number = {2005-02},
  address = {Computer Science and Engineering Department},
  month = FEB
}

@ARTICLE{Albe05,
  author = {M. S. Alber and T. Glimm and H. G. E. Hentschel and B. Kazmiercazk
	and S. A. Newman},
  title = {Stability of $n$-Dimensional Patterns in a Generalized Turing System:
	Implications for Biological Pattern Formation},
  journal = {Nonlinearity},
  year = {2005},
  volume = {18},
  pages = {125--138},
  number = {1}
}

@UNPUBLISHED{AHKN0x,
  author = {M. S. Alber and H. G. E. Hentschel and B. Kazmiercazk and S. A. Newman},
  title = {Existence of Solutions to a New Model of Biological Pattern Formation},
  note = {{\em Journal of Mathematical Analysis and Applications}, in press.},
  year = {2005}
}

@TECHREPORT{ArCI05,
  author = {Kedar Aras and Trevor Cickovski and Jes\'{u}s A.\ Izaguirre},
  title = {Empirical Evaluation of Design Patterns in Scientific Application},
  institution = {Univ. of Notre Dame},
  year = {2005},
  number = {TR 2005-08},
  note = {Preprint: \url{ftp://ftp.cse.nd.edu/pub/Reports/2005/TR-2005-08.pdf}}
}

@ARTICLE{BaLS05,
  author = {Eric Barth and Ben Leimkuhler and Chris Sweet},
  title = {Approach to Thermal Equilibrium in Biomolecular Simulation},
  journal = {FIXME},
  year = {2005},
  note = {To appear in \emph{{P}roc. of {A}lgorithms for {M}acromolecular {M}odeling
	{IV}}. Lecture Notes in Computational Science and Engineering (LNCSE).
	Springer Verlag. New York and Berlin.}
}

@ARTICLE{BerS05,
  author = {A.~Berezhkovskii and A.~Szabo},
  title = {One dimensional reaction coordinates for diffusive activated rate
	processes in many dimensions},
  journal = JCP,
  year = {2005},
  volume = {122},
  pages = {014503}
}

@ARTICLE{BeCH05,
  author = {R.~Best and Y.~Chen and G.~Hummer},
  title = {Slow Protein conformational dynamics from Multiple Experimental Structures:
	The Helix/Sheet transition of Arc Repressor},
  journal = STR,
  year = {2005},
  volume = {13},
  pages = {1755-1763}
}

@ARTICLE{BeCK05,
  author = {Robert B. Best and Jane Clarke and Martin Karplus},
  title = {What Contributions to Protein Side-Chain Dynamics are Probed by {NMR}
	Experiments? A Molecular Dynamics Simulation Analysis},
  journal = {J. Mol. Biol.},
  year = {2005},
  volume = {349},
  pages = {185--203}
}

@ARTICLE{BeHu05,
  author = {Robert B. Best and Gerhard Hummer},
  title = {Reaction coordinates and rates from transition paths},
  journal = PNAS,
  year = {2005},
  volume = {102},
  pages = {6732--6737}
}

@MISC{BIOS,
  author = {BioSPICE},
  title = {BioSPICE Community Web Site: Biology in silico},
  year = {2005},
  note = {\url{https://community.biospice.org}}
}

@CONFERENCE{BlAW05,
  author = {P. Blikstein and D. Abrahamson and U. Wilensky},
  title = {{N}et{L}ogo: {W}here we are, where we're going},
  booktitle = {Proceedings of the annual meeting of Interaction Design and Children},
  year = {2005},
  publisher = {Boulder, CO}
}

@ARTICLE{Bou+05,
  author = {Guillaume Bouviginies and Pau Bernad{\'o} and Sebastian Meier and
	Kyuil Cho and Stephan Grzesiek and Rafael Br{\"u}schweiler and Martin
	Blackledge},
  title = {Identification of Slow Correlated Motions in Proteins Using Residual
	Dipolar and Hydrogen-Bond Scalar Couplings},
  journal = {PNAS},
  year = {2005},
  volume = {102},
  pages = {13885--13890}
}

@MISC{CSHA05,
  author = {C\#},
  title = {C\# Corner},
  year = {2005},
  note = {\url{http://www.c-sharpcorner.com}}
}

@ARTICLE{Calv05,
  author = {F. Calvo},
  title = {All-exchanges parallel tempering},
  journal = JCP,
  year = {2005},
  volume = {123},
  pages = {124106}
}

@MISC{VIRT,
  author = {Virtual~Cell},
  title = {National Resource for Cell Analysis and Modeling},
  year = {2005},
  note = {\url{http://www.nrcam.uchc.edu}}
}

@MISC{CELL,
  author = {Cell-O-Sim},
  title = {Cell-O-Sim website},
  year = {2005},
  note = {\url{http://mbi.dkfz-heidelberg.de/projects/cellsim/cellosim}}
}

@ARTICLE{Chat05,
  author = {R.\ Chaturvedi and C.\ Huang and B.\ Kazmierczak and T.\ Schneider
	and J.~A.\ Izaguirre and S.~A.\ Newman and J.~A.\ Glazier and M.~S.\
	Alber},
  title = {On Multiscale Approaches to 3-Dimensional Modeling of Morphogenesis},
  journal = {J. Roy. Soc. Interface},
  year = {2005},
  volume = {2},
  pages = {237--253}
}

@ARTICLE{CRYB05,
  author = {C.~Chennubhotla and A.~J.~Rader and L.~Yang and I.~Bahar},
  title = {Elastic Network models for understanding biomolecular machinery:from
	enzymes to supramolecular assemblies},
  journal = PHCB,
  year = {2005},
  volume = {2},
  pages = {S173-S180}
}

@ARTICLE{Cick05,
  author = {T.\ Cickovski and C.\ Huang and R.\ Chaturvedi and T.\ Glimm and
	H.~G. E.\ Hentschel and M.~S.\ Alber and J.~A.\ Glazier and S.~A.\
	Newman and J.~A.\ Izaguirre},
  title = {A Framework for Three-Dimensional Simulation of Morphogenesis},
  journal = TCBB,
  year = {2005},
  volume = {2},
  pages = {273--288},
  number = {4}
}

@ARTICLE{Cick0xa,
  author = {T. Cickovski and J. A. Izaguirre},
  title = {BIOLOGO, A Domain-Specific Language For Morphogenesis},
  journal = {ACM Transations on Programming Languages and Systems},
  year = {2005},
  note = {To be submitted, preprint at \url{http://www.nd.edu/~tcickovs/acmtr2e.pdf}}
}

@ARTICLE{Cick0xb,
  author = {T. Cickovski and J. A. Izaguirre},
  title = {BIOLOGO, A Domain-Specific Language For Morphogenesis},
  journal = {Bioinformatics},
  year = {2005},
  note = {Submitted, preprint at \url{http://www.nd.edu/~tcickovs/document.pdf}}
}

@UNPUBLISHED{CiIz0x,
  author = {Trevor Cickovski and Jes\'{u}s A.\ Izaguirre},
  title = {{BIOLOGO}: A Domain-Specific Language for Morphogenesis},
  note = {In preparation. Manuscript available at \url{http://www.nd.edu/~tcickovs/document.pdf}},
  year = {2005}
}

@ARTICLE{CHMI05,
  author = {Michael~S. Crocker and Scott~S. Hampton and Thierry Matthey and Jes{\'u}s~A.
	Izaguirre},
  title = {{MDS}im{A}id: {A}utomatic Parameter Optimization in Fast Electrostatic
	Algorithms},
  journal = JCC,
  year = {2005},
  volume = {26},
  pages = {1021--1031}
}

@UNPUBLISHED{DaGl05,
  author = {D. Dan and J. A. Glazier},
  title = {Study of diffusion and chemotaxis in cell motion using cellular Potts
	model},
  note = {Submitted to {\it Phys. Rev. E.}},
  year = {2005}
}

@BOOK{DeDo05,
  title = {Cellular Automaton Modeling of Biological Pattern Formation},
  publisher = {Birkhauser},
  year = {2005},
  author = {A. Deutsch and S. Dormann},
  address = {Boston}
}

@BOOK{FoKe03,
  author = {Ian Foster and Carl Kesselman},
  title = {The Grid 2: Blueprint for a New Computing Infrastructure},
  publisher = {Morgan Kaufmann},
  year = {2003},
  edition = {2nd},
  address = {San Fransico, California}
}

@ARTICLE{EaDe05,
  author = {David J. Earl and Michael W. Deem},
  title = {Parallel tempering: Theory, applications, and new perspectives},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2005},
  volume = {7},
  pages = {3910--3916}
}

@ARTICLE{Elbe05,
  author = {R. Elber},
  title = {Long-timescale simulation methods},
  journal = COSB,
  year = {2005},
  volume = {15},
  pages = {151--156}
}

@ARTICLE{EnSD05,
  author = {R. D. Engle and R. D. Skeel and M. Drees},
  title = {Monitoring energy drift with shadow {H}amiltonians},
  journal = JCMP,
  year = {2005},
  volume = {206},
  pages = {432--452},
  number = {2}
}

@ARTICLE{ErBo05,
  author = {Titus S. Van Erp and Peter G. Bolhuis},
  title = {Elaborating Transition Interface Sampling Methods},
  journal = jcmp,
  year = {2005},
  volume = {205},
  pages = {157--181}
}

@BOOK{FORG05,
  title = {Biological Physics of the Developing Embryo},
  publisher = {Cambridge University Press},
  year = {2005},
  author = {G. Forgacs and S. A. Newman},
  address = {Cambridge}
}

@ARTICLE{GAFL05,
  author = {Emilio Gallicchio and Michael Andrec and Anthony K. Felts and Ronald
	M. Levy},
  title = {Temperature Weighted Histogram Analysis Method, Replica Exchange,
	and Transition},
  journal = JCP,
  year = {2005},
  volume = {109},
  pages = {6722--6731}
}

@MISC{Gnup05,
  author = {Gnuplot.py},
  title = {Gnuplot.py on SourceForge},
  year = {2005},
  note = {\url{http://gnuplot-py.sourceforge.net}}
}

@ARTICLE{HaSM05,
  author = {D.~Hamelberg and T.~Shen and J.~Andrew Mccammon},
  title = {Relating kinetic rates and local energetic roughness by accelerated
	molecular-dynamics simulations},
  journal = JCP,
  year = {2005},
  volume = {122},
  pages = {24411031--4}
}

@ARTICLE{HBSL05,
  author = {Liegi Hu and Mark L. Benson and Richard D. Smith and Michael G. Lerner
	and Heather A. Carlson},
  title = {Binding MOAD (Mother Of All Databases)},
  journal = PRO,
  year = {2005},
  volume = {Online Preprint},
  pages = {xxxx--xxxx}
}

@ARTICLE{IzHM05,
  author = {Jes{\'u}s~A. Izaguirre and Scott~S. Hampton and Thierry Matthey},
  title = {Parallel multigrid summation for the {N}-body problem},
  journal = JPDC,
  year = {2005},
  volume = {65},
  pages = {949--962}
}

@ARTICLE{KBC+05,
  author = {K. Kennedy and B. Broom and A. Chauhan and R. J. Fowler and J. Garvin
	and C. Koelbel and C. McCosh and J. Mellor-Crummey},
  title = {Telescoping Languages: A System for Automatic Generation of Domain
	Languages},
  journal = {Proceedings of the IEEE},
  year = {2005},
  volume = {93},
  pages = {387--408},
  number = {2}
}

@ARTICLE{KnHL05,
  author = {W. Knight and W. Hill and J. S. Lodmell},
  title = {Ribosome Builder: A software project to simulate the ribosome},
  journal = {Computational Biology and Chemistry},
  year = {2005},
  volume = {29},
  pages = {163--174},
  number = {2}
}

@ARTICLE{KoKo05,
  author = {A. Kone and D. A. Kofke},
  title = {Selection of temperature intervals for parallel-tempering simulations},
  journal = {J. Chem. Phys.},
  year = {2005},
  volume = {122},
  pages = {206--101}
}

@ARTICLE{Kofk93,
  author = {D. A. Kofke},
  title = {Direct evaluation of phase coexistence by molecular simulation via integration along the saturation line},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {98},
  pages = {4149--4162}
}


@ARTICLE{LeSw05,
  author = {B.~J.~Leimkuhler and C.~R.~Sweet},
  title = {{H}amiltonian formulation for recursive multiple thermostats in a
	common timescale},
  journal = SIADS,
  year = {2005},
  volume = {4},
  pages = {187--216},
  number = {1}
}

@ARTICLE{Leom05,
  author = {A.~Leo-Macias and P.~Lopez-Romero and D.~Lupyan and D.~Zerbino and
	A.~R.~Ortiz},
  title = {An Analysis of Core Deformations in Protein Superfamilies},
  journal = BJ,
  year = {2005},
  volume = {88},
  pages = {1291--1299}
}

@MISC{LMX05,
  author = {LMX},
  title = {{L}{M}{X} {X}{M}{L} to {C}++ {B}inding {C}ode {G}enerator},
  year = {2005},
  note = {\url{http://tech-know-ware.com/lmx/}}
}

@ARTICLE{Ma05,
  author = {J.~Ma},
  title = {Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics
	of Biomolecular Complexes},
  journal = STR,
  year = {2005},
  volume = {13},
  pages = {373--380}
}

@ARTICLE{MarK05,
  author = {P.~Maragakis and M.~Karplus},
  title = {Large {A}mplitude {C}onformational {C}hange in {P}roteins {E}xplored
	with a {P}lastic {N}etwork {M}odel:{A}denylate {K}inase},
  journal = JMB,
  year = {2005},
  volume = {352},
  pages = {807-822}
}

@MISC{MATH05,
  author = {Mathematica},
  title = {The Way The World Calculates},
  howpublished = {\url{http://www.wolfram.com/products/mathematica}},
  year = {2005},
  annote = {Mathematica Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{MATP05,
  author = {Matplotlib},
  title = {Matlab Style Python Plotting},
  howpublished = {\url{http://matplotlib.sourceforge.net/}},
  year = {2005},
  annote = {Matplotlib Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{MeGl05,
  author = {R.~M. H. Merks and J.~A. Glazier},
  title = {A cell-centered approach to developmental biology},
  journal = {Phys. A},
  year = {2005},
  volume = {352},
  pages = {113--130}
}

@MISC{MODU05,
  author = {Modula-3},
  title = {Modula-3 Home Page},
  year = {2005},
  note = {\url{http://research.compaq.com/SRC/modula-3/html/home.html}}
}

@ARTICLE{MRG+05,
  author = {J.~C. M. Mombach and D.~Robert and F.~Graner and G.~Gillet and G.~L.
	Thomas and M.~Idiart and J.~P. Rieu},
  title = {Rounding of aggregates of biological cells: experiments and simulations},
  journal = {Physica A},
  year = {2005},
  volume = {352},
  pages = {525--534}
}

@MISC{NETL05,
  author = {NetLogo},
  title = {NetLogo Home Page},
  howpublished = {\url{http://ccl.northwestern.edu/netlogo}},
  year = {2005},
  annote = {NetLogo Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{NJKG05,
  author = {H. Nguyen and M. Jager and J. W. Kelly and M. Gruebele},
  title = {Engineering a Beta-Sheet Protein Toward the Folding Speed Limit},
  journal = {J. Phys. Chem. B},
  year = {2005},
  volume = {109},
  pages = {15182--15186},
  abstract = {Recent experimental studies have shown that a.-helical proteins can
	approach the folding "speed limit", where folding switches from an
	activated to a downhill process in free energy. beta-sheet proteins
	are generally thought to fold more slowly than helix bundles. However,
	based on studies of hairpins, folding should still be able to approach
	the microsecond time scale. Here we demonstrate how the hPin1 WW
	domain, a triple-stranded beta-sheet protein with a sharp thermodynamic
	melting transition, can be engineered toward the folding "speed limit"
	without a significant loss in thermal denaturation cooperativity.}
}

@MISC{Nump05,
  author = {NumPy},
  title = {Numerical Python Libraries},
  howpublished = {\url{http://numeric.scipy.org}},
  year = {2005},
  annote = {NumPy},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{Perl05,
  author = {Perl},
  title = {The Perl Directory: About Perl},
  year = {2005},
  note = {\url{http://www.perl.org}}
}

@ARTICLE{PrPC05,
  author = {C. Predescu and M. Predescu and C. V. CioBanu},
  title = {On the Efficiency of Exchange in Parallel Tempering {M}onte {C}arlo
	Simulations},
  journal = {J. Phys. Chem. B},
  year = {2005},
  volume = {109},
  pages = {4189}
}

@ARTICLE{RaCP05,
  author = {N. Rathore and M. Chopra and J. J. de Pablo},
  title = {Optimal allocation of replicas in parallel tempering simulations},
  journal = {J. Chem. Phys.},
  year = {2005},
  volume = {122},
  pages = {24111}
}

@ARTICLE{RVNW05,
  author = {W.~Ren and E.~Vanden-Eijnden and P.~Maragakis and E.~WN},
  title = {Transition pathways in complex systems: Application of the finite-temperature
	string method to the alanine dipeptide},
  journal = JCP,
  year = {2005},
  volume = {123},
  pages = {AN 134109},
  number = {13}
}

@ARTICLE{RheP05,
  author = {Y.~M.~Rhee and V.~S.~Pande},
  title = {One-Dimensional Reaction Coordinate and the corresponding Potential
	of Mean force from Commitment Probability distribution},
  journal = JPCB,
  year = {2005},
  volume = {109},
  pages = {6780--6786}
}

@ARTICLE{RheP06,
  author = {Y.~M.~Rhee and V.~S.~Pande},
  title = {On the role of chemical detail in simulating protein folding kinetics},
  journal = JCP,
  year = {2006},
  volume = {323},
  pages = {66--77}
}

@ARTICLE{RoAT05,
  author = {Lula Rosso and Jerry B. Abrams and Mark E. Tuckerman},
  title = {Mapping the Backbone Dihedral Free-Energy Surfaces in Small Peptides
	in Solution Using Adiabatic Free-Energy Dynamics},
  journal = JPCB,
  year = {2005},
  volume = {109},
  pages = {4162--4167}
}

@MISC{RUBY05,
  author = {Ruby},
  title = {Ruby Home Page},
  year = {2005},
  note = {\url{http://www.ruby-lang.org}}
}

@ARTICLE{SBTH05,
  author = {S.~A.~Showalter and N.~A.~Baker and C.~Tang and K.~B.~Hall},
  title = {Iron responsive element {RNA} flexibility described by {NMR} and
	isotropic reorientational eigenmode dynamics},
  journal = JBNMR,
  year = {2005},
  volume = {32},
  pages = {179-193}
}

@MISC{SOUR05,
  author = {SourceForge},
  title = {SourceForge.net},
  year = {2005},
  note = {\url{http://www.sourceforge.net}}
}

@ARTICLE{WeRV05,
  author = {E.~Weinan and W.~Q.~Ren and E.~Vanden-Eijnden},
  title = {Finite temperature string method for the study of rare events},
  journal = JPCB,
  year = {2005},
  volume = {109},
  pages = {6688--6693},
  number = {14}
}

@PHDTHESIS{Wong05,
  author = {S. Wong},
  title = {A Cursory Study of the Thermodynamics and Mechanical Properties of
	{M}onte-{C}arlo Simulations of the Ising Model},
  school = {University of Notre Dame},
  year = {2005},
  address = {Notre Dame, Indiana, USA}
}

@ARTICLE{WNJM05,
  author = {Christopher J. Woods and Muan Hong Ng and Steven Johnston and Stuart
	E. Murdock and Bing Wu and Kaihsu Tai and Hans Fangohr and Paul Jeffreys
	and Simon Cox and Jeremy G. Frey and Mark S.P. Sansom and Jonathan
	W. Essex},
  title = {Grid computing and biomolecular simulation},
  journal = {Phil. Trans. of The Royal Society A},
  year = {2005},
  volume = {363},
  pages = {2017--2035},
  number = {1833}
}

@INPROCEEDINGS{WBTS05,
  author = {J. M. Wozniak and P. Brenner and D. Thain and A. Striegel and J.
	A. Izaguirre},
  title = {Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations},
  booktitle = {IEEE International Symposium on High Performance Distributed Computing
	Proceedings},
  year = {2005},
  note = {In Press},
  owner = {Paul}
}

@UNPUBLISHED{WoBr0x,
  author = {J.~M.\ Wozniak and P.\ Brenner and D.\ Thain and A.\ Striegel and
	J.~A.\ Izaguirre},
  title = {Generosity and Gluttony in {GEMS}: {G}rid {E}nabled {M}olecular {S}imulations},
  note = {\emph{Proc. 14th IEEE International Symposium on High Performance
	Distributed Computing (HPDC-14)}. Preprint: \url{http://www.nd.edu/~izaguirr/papers/wozniakj_gems.pdf}},
  year = {2005}
}

@INPROCEEDINGS{WSSI05,
  author = {J.~M.\ Wozniak and A.\ Striegel and D.\ Salyers and J.~A.\ Izaguirre},
  title = {{GIPSE}: Streamlining the Management of Simulation on the Grid},
  booktitle = {Proc. of the 38th Annual Simulation Symposium ANSS 05},
  year = {2005},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/wozniakj_gipse.pdf}},
  annote = {San Diego, CA, April 2-8, 2005}
}

@MISC{COMPUCELL,
  author = {{COMPUCELL}},
  title = {\textsc{Compu{C}ell}: A Framework For Three-Dimensional Simulation
	of Morphogenesis},
  howpublished = {\url{http://sourceforge.net/projects/compucell/}},
  month = SEP,
  year = {2004},
  note = {350 downloads from Apr. 2003 - Feb. 2005},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{PROTOMOL,
  author = {{PROTOMOL}},
  title = {\textsc{Proto{M}ol}: An Object Oriented Framework for Molecular Dynamics},
  howpublished = {\url{http://sourceforge.net/projects/protomol/}},
  month = SEP,
  year = {2004},
  note = {868 downloads from Sept. 2003 - Feb. 2005},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{MDSIMAID,
  author = {\textsc{MDSimAid}},
  title = {{M}olecular {D}ynamics {S}imulation {A}id},
  howpublished = {\url{http://mdsimaid.cse.nd.edu/}},
  month = AUG,
  year = {2004},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{PBCAID,
  author = {{PBCAID}},
  title = {PBCAID},
  howpublished = {\url{http://monod.biomath.nyu.edu/index/software.html}},
  month = AUG,
  year = {2004},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{CSE598K,
  author = {CSE598K},
  title = {{CSE} 598k: {C}omputational Methods in Biomolecular Modeling},
  howpublished = {\url{http://www.cse.nd.edu/courses/cse598k/www/}},
  month = JUL,
  year = {2004},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{LCLS,
  author = {Jes{\'u}s A. Izaguirre},
  title = {{L}aboratory~for~{C}omputational~{L}ife~{S}ciences},
  howpublished = {\url{http://www.nd.edu/~lcls}},
  month = JUL,
  year = {2004},
  annote = {LCLS research group home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{BioSimGrid,
  author = {Mark Sansom},
  title = {Bio{S}im{G}rid},
  howpublished = {\url{http://www.biosimgrid.org}},
  month = JUL,
  year = {2004},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{DIST04,
  author = {distcc},
  title = {distcc, A fast, free distributed C/C++ compiler},
  year = {2004},
  note = {\url{http://distcc.samba.org}}
}

@MISC{RDF04,
  author = {Resource Description Framework (RDF)},
  title = {W3C Semantic Web Activity},
  howpublished = {\url{http://www.w3.org/RDF}},
  year = {2004},
  annote = {Resource Description Framework (RDF)},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{AlJK04,
  author = {M.~S. Alber and Y.~Jiang and M.~A. Kiskowski},
  title = {Lattice gas cellular automaton model for rippling and aggregation
	in Myxobacteria},
  journal = {Physica D},
  year = {2004},
  volume = {191},
  pages = {343--358},
  number = {3--4}
}

@ARTICLE{AlKJ04,
  author = {M. S. Alber and M. A. Kiskowski and Y. Jiang},
  title = {Two-Stage aggregate formation via streams in Myxobacteria},
  journal = {Phys. Rev. Lett.},
  year = {2004},
  volume = {93},
  pages = {068301}
}

@ARTICLE{Ber+04,
  author = {Pau Bernad{\'o} and Miguel X. Fernandes and Doris M. Jacobs and Klaus
	Fiebig and Jos{\'e} Garc{\'{\i}}a de la Torre and Miquel Pons},
  title = {Interpretation of {NMR} Relaxation Properties of Pin1, a Two-Domain
	Protein, Based on {B}rownian Dynamic Simulations},
  journal = {J. of Biomolecular NMR},
  year = {2004},
  volume = {29},
  pages = {21--35}
}

@INCOLLECTION{Chat04,
  author = {R.\ Chaturvedi and C.\ Huang and J.~A.\ Izaguirre and S.~A.\ Newman
	and J.~A.\ Glazier and M.~S.\ Alber},
  title = {A Hybrid Discrete-Continuum Model for {3-D} Skeletogenesis of the
	Vertebrate Limb},
  booktitle = {Cellular Automata: 6th International Conference on Cellular Automata
	for Research and Industry, ACRI 2004, Amsterdam, The Netherlands,
	October 25-28, 2004},
  publisher = {Springer Verlag},
  year = {2004},
  editor = {Peter M.~A.\ Sloot and Bastien Chopard and Alfons G.\ Hoekstra},
  volume = {3305},
  series = {Lecture Notes in Computer Science},
  pages = {543--552},
  address = {Berlin Heidelberg},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/Chat0xb.pdf}}
}

@MASTERSTHESIS{Cick04,
  author = {Trevor Cickovski},
  title = {BioLogo, A Domain-Specific Language For Morphogenesis},
  school = {University of Notre Dame},
  year = {2004},
  address = {Notre Dame, Indiana, USA}
}

@TECHREPORT{CiMI04,
  author = {Trevor Cickovski and Thierry Matthey and Jes\'{u}s A.\ Izaguirre},
  title = {Design Patterns for Scientific Software},
  institution = {Univ. of Notre Dame},
  year = {2004},
  number = {TR-2004-29},
  note = {Preprint: \url{ftp://ftp.cse.nd.edu/pub/Reports/2004/TR-2004-29.pdf}}
}

@ARTICLE{CLMK04,
  author = {Q.~Cui and G.~Li and J.~P.~Ma and M.~Karplus},
  title = {A normal mode analysis of structural plasticity in the biomolecular
	motor {F}-1-{ATP}ase},
  journal = JMB,
  year = {2004},
  volume = {340},
  pages = {345--372},
  number = {2}
}

@ARTICLE{VoMe04,
  author = {G.~von Dassow and E.~Meir},
  title = {Exploring modularity with dynamical models of gene networks, In {G}.
	{S}chlosser, {G}.{P}. {W}agner ({E}ds.)},
  journal = {Modularity in Development and Evolution},
  year = {2004},
  pages = {244--287},
  publisher = {Univ. Chicago Press, Chicago}
}

@ARTICLE{FarE04,
  author = {A.~K.~Faradjian and R.~Elber},
  title = {Computing time scales from reaction coordinates by milestoning},
  journal = JCP,
  year = {2004},
  volume = {120},
  pages = {10880-10889},
  number = {23}
}

@ARTICLE{HaMM04,
  author = {D.~Hamelberg and J.~Mongan and J.~A.~McCammon},
  title = {Accelerated molecule dynamics: A promising and efficient simulation
	method for biomolecules},
  journal = JCP,
  year = {2004},
  volume = {120},
  pages = {11919--11929},
  number = {24}
}

@INCOLLECTION{HaIz04,
  author = {Scott S. Hampton and Jesus A. Izaguirre},
  title = {Improved Sampling for Biological Molecules Using Shadow Hybrid {M}onte
	{C}arlo},
  booktitle = {4th International Conference on Computational Science, Krak{\'o}w,
	Poland},
  publisher = {Springer-Verlag},
  year = {2004},
  editor = {M. Bubak and G. D.~von~Albada and P. M.~A.~Sloot; J. J.~Dongarra},
  volume = {3037},
  series = {{LNCS}},
  pages = {268--274},
  address = {New York}
}

@ARTICLE{HaCa04,
  author = {T.~Hayashi and R.~Carthew},
  title = {Surface mechanics mediate pattern formation in the developing retina},
  journal = {Nature},
  year = {2004},
  volume = {431},
  pages = {647--652},
  number = {7009}
}

@ARTICLE{Hent04,
  author = {H.~G. E. Hentschel and T.~Glimm and J.~A. Glazier and S.~A. Newman},
  title = {Dynamical mechanisms for skeletal pattern formation in the vertebrate
	limb},
  journal = {Proc. R. Soc. Lond. B Biol. Sci.},
  year = {2004},
  volume = {271},
  pages = {1713--1722},
  number = {10}
}

@UNPUBLISHED{HXMC04,
  author = {Y.~Huang and X.~Xiang and G.~Madey and S.~Cabaniss.},
  title = {Agent-based Scientific Simulation Using Java/Swarm, J2EE, RDBMS and
	Automatic Management Techniques.},
  note = {Preprint.},
  year = {2004}
}

@ARTICLE{Palm04,
  author = {Arthur G. Palmer III},
  title = {{NMR} Characterization of the Dynamics of Biomacromolecules},
  journal = {CR},
  year = {2004},
  volume = {104},
  pages = {3623--3640}
}

@ARTICLE{ICH+04,
  author = {J.~A.\ Izaguirre and R.\ Chaturvedi and C.\ Huang and T.\ Cickovski
	and J.\ Coffland and G.\ Thomas and G.\ Forgacs and M.~S.\ Alber
	and G.\ Hentschel and S.~A.\ Newman and J.~A.\ Glazier},
  title = {Compu{C}ell, a multimodel framework for simulation of morphogenesis},
  journal = {Bioinformatics},
  year = {2004},
  volume = {20},
  pages = {1129--1137},
  eprint = {http://bioinformatics.oupjournals.org/cgi/reprint/20/7/1129.pdf},
  url = {http://bioinformatics.oupjournals.org/cgi/content/abstract/20/7/1129}
}

@ARTICLE{IzHa04,
  author = {Jes\'us A. Izaguirre and Scott S. Hampton},
  title = {Shadow Hybrid {M}onte {C}arlo: An Efficient Propagator in Phase Space
	of Macromolecules},
  journal = JCMP,
  year = {2004},
  volume = {200},
  pages = {581--604},
  number = {2}
}

@ARTICLE{KarG04,
  author = {M.~Karplus and Y.~Q.~Gao},
  title = {Biomolecular motors: the {F}-1-{ATP}ase paradigm},
  journal = COSB,
  year = {2004},
  volume = {14},
  pages = {250--259}
}

@ARTICLE{KAT+04,
  author = {M. A. Kiskowski and M. S. Alber and G. L. Thomas and J. A. Glazier
	and N. B. Bronstein and J. Pu and S. A. Newman},
  title = {Interplay between activator-inhibitor coupling and cell-matrix adhesion
	in a cellular automaton model for chondrogenic patterning},
  journal = {Dev. Biol.},
  year = {2004},
  volume = {271},
  pages = {372--387},
  number = {2}
}

@ARTICLE{KiJA04,
  author = {M.~A. Kiskowski and Y.~Jiang and M.~S. Alber},
  title = {Role of streams in Myxobacteria aggregate formation},
  journal = {Physical Biology},
  year = {2004},
  volume = {1},
  pages = {173--183},
  number = {3}
}

@ARTICLE{Kofk04,
  author = {D. A. Kofke},
  title = {Getting the most from molecular simulation},
  journal = MP,
  year = {2004},
  volume = {102},
  pages = {405--420},
  number = {4}
}

@ARTICLE{KrDS04,
  author = {Bryan A. Krantz and Robin S. Dothager and Tobin R. Sosnick},
  title = {Discerning the Structure and Energy of {MultipleTransition} States
	in Protein Folding Using Psi-Analysis},
  journal = {J. Mol. Biol.},
  year = {2004},
  volume = {337},
  pages = {463--475},
  abstract = {We quantify the degree to which folding occurs along a complex landscape
	with structurally distinct pathways using c-analysis in combination
	with a protein engineering method that identifies native, non-covalent
	polypeptide interactions and their relative populations at the rate-limiting
	step. By probing the proximity of two specific partners, this method
	is extremely well-suited for comparison to theoretical simulations.
	Using ubiquitin as a model system, we detect individual pathways
	with siteresolved resolution, demonstrating that the protein folds
	through a native-like transition state ensemble with a common nucleus
	that contains heterogeneous features on its periphery. The consensus
	transition state topology has part of the major helix docked against
	four properly aligned b-strands. However, structural heterogeneity
	exists in the transition state ensemble, wherein peripheral regions
	are differentially populated according to their relative stability.
	Pathway diversity reflects the variable order of formation of these
	peripheral elements, which radiate outward from the common nucleus.
	These results, which show only moderate agreement with traditional
	mutational f-analysis, provide an extraordinarily detailed and quantitative
	description of protein folding.}
}

@BOOK{LeRe04,
  title = {Simulating {H}amiltonian Dynamics},
  publisher = {Cambridge University Press},
  year = {2004},
  author = {Benedict Leimkuhler and Sebastian Reich},
  remark = {ISBN: 0521772907}
}

@ARTICLE{LeSw04,
  author = {B.~J.~ Leimkuhler and C.~R.~ Sweet},
  title = {The Canonical ensemble via Symplectic Integrators using {N}os\'e
	and {N}os\'e-{P}oincar\'e chains},
  journal = JCP,
  year = {2004},
  volume = {121},
  pages = {108--116},
  number = {1}
}

@ARTICLE{LlHN04,
  author = {Catherine M. Lloyd and Matt D. B. Halstead and Poul F. Nielsen},
  title = {CellML: Its Future, Present and Past},
  journal = {Progress in Biophysics and Molecular Biology},
  year = {2004},
  volume = {85},
  pages = {433--450},
  number = {2--3}
}

@ARTICLE{Lu04,
  author = {Kun Ping Lu},
  title = {Pinning down cell signaling, cancer, and Alzheimer's disease},
  journal = {Trends in Biochemical Sciences},
  year = {2004},
  volume = {29},
  pages = {200--209},
  number = {4}
}

@ARTICLE{MACK04,
  author = {A. D. {MacKerell Jr.}},
  title = {Empirical Force Fields for Biological Macromolecules: Overview and
	Issues},
  journal = JCC,
  year = {2004},
  volume = {25},
  pages = {1584--1604},
  annote = {To cite CHARMM force field, cite this paper and MACK92}
}

@ARTICLE{Matt04,
  author = {Thierry Matthey and Trevor Cickovski and Scott~S. Hampton and Alice
	Ko and Qun Ma and Matthew Nyerges and Troy Raeder and Thomas Slabach
	and Jes\'{u}s A. Izaguirre},
  title = {\textsc{{P}roto{M}ol}: {A}n Object-Oriented Framework for Prototyping
	Novel Algorithms for Molecular Dynamics},
  journal = ACMTMS,
  year = {2004},
  volume = {30},
  pages = {237--265},
  number = {3}
}

@ARTICLE{Mein04,
  author = {H. Meinhardt},
  title = {Pathways and building blocks: {R}eview of ``Modularity in Development
	and Evolution,'' {G}. {S}chlosser, {G}. {P}. {W}agner ({E}ds.).},
  journal = {\it Nature},
  year = {2004},
  volume = {430},
  pages = {970},
  number = {7003}
}

@INPROCEEDINGS{MeNG04,
  author = {R.~M.~H.~Merks and S.~A.~Newman and J.~A.~Glazier},
  title = {Cell-oriented modeling of {\it in vitro} capillary development},
  booktitle = {Proceedings of Cellular Automata: 6th International Conference on
	Cellular Automata for Research and Industry, ACRI 2004},
  year = {2004},
  editor = {P. M. A. Sloot and B. Chopard and A. G. Hoekstra},
  volume = {3305},
  pages = {425--434},
  publisher = {Springer-Verlag, Berlin}
}

@ARTICLE{Okam04,
  author = {Yuko Okamoto},
  title = {Generalized-ensemble algorithms: enhanced sampling techniques for
	{M}onte {C}arlo and molecular dynamics simulations},
  journal = {J. Molecular Graphics and Modelling},
  year = {2004},
  volume = {22},
  pages = {425--439}
}

@MISC{Pyth04,
  author = {Python},
  title = {Python Programming Language},
  year = {2004},
  note = {\url{http://www.python.org}}
}

@ARTICLE{Pusc04,
  author = {Markus P{\"u}schel and Bryan Singer and Jianxin Xiong and Jos{\'e}
	Moura and Jeremy Johnson and David Padua and Manuela Veloso and Robert
	W. Johnson},
  title = {{SPIRAL}: {A} Generator for Platform-Adapted Libraries of Signal
	Processing Algorithms},
  journal = IJHPCA,
  year = {2004},
  volume = {18},
  pages = {21--45},
  number = {1},
  nremark = {A recommender example.}
}

@ARTICLE{RaSc04,
  author = {Ravi Radhakrishnan and Tamar Schlick},
  title = {Biomolecular free energy profiles by a shooting/umbrella sampling
	protocol, ``{BOLAS}''},
  journal = JCP,
  year = {2004},
  volume = {121},
  pages = {2436--2444},
  number = {5}
}

@ARTICLE{RaSc04a,
  author = {Ravi Radhakrishnan and Tamar Schlick},
  title = {Orchestration of cooperative events in DNA synthesis and repair mechanism
	unraveled by transition path sampling of DNA polymerase beta's closing.},
  journal = PNAS,
  year = {2004},
  volume = {101},
  pages = {5970--5975}
}

@TECHREPORT{GIPS04,
  author = {A.\ Striegel and M.\ Shorts and E.\ Stuntebeck and D.\ Salyers and
	J.~A.\ Izaguirre},
  title = {{GIPSE}: A Toolset for Streamlining the Management Aspects of the
	Grid for Simulation-based Research},
  institution = {University of Notre Dame},
  year = {2004},
  number = {TR 04-16}
}

@BOOK{SUND04,
  title = {Oracle 9i Programming: A Primer},
  publisher = {Addison-Wesley},
  year = {2004},
  author = {R. Sunderraman}
}

@ARTICLE{TMWN04,
  author = {Kaihsu Tai and Stuart Murdock and Bing Wu and Muan Hong Ng and Steven
	Johnston and Hans Fangohr and Simon Cox and Paul Jeffreys and Johnathan
	W. Essex and Mark Sansom},
  title = {BioSimGrid: towards a worldwide repository for biomolecular simulations},
  journal = {Org. Biomol. Chem},
  year = {2004},
  volume = {2},
  pages = {3219--3221}
}

@MISC{TCE,
  author = {TCE},
  title = {The Tensor Contraction Engine},
  howpublished = {\url{http://www.cse.ohio-state.edu/~gb/TCE}},
  year = {2004},
  annote = {TCE Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{VeKu04,
  author = {S. Vercruysse and M. Kuiper},
  title = {Simulating genetic networks made easy: network construction with
	simple building blocks},
  journal = {Bioinformatics},
  year = {2004},
  volume = {21},
  pages = {269--271},
  number = {2}
}

@ARTICLE{WUKC04,
  author = {O. Wolkenhauer and M. Ullah and W. Kolch and K.-{H}. Cho},
  title = {Modelling and simulation of intracellular dynamics: Choosing an appropriate
	framework},
  journal = {IEEE Transactions on NanoBioScience},
  year = {2004},
  volume = {3},
  pages = {200--207},
  number = {3}
}

@MISC{XIMP04,
  author = {Ximpo.com},
  title = {Research and Development Server},
  year = {2004},
  note = {\url{http://www.ximpo.com/Products/RnD_server}}
}

@INPROCEEDINGS{MaIS03b,
  author = {Qun Ma and Jes{\'u}s A.\ Izaguirre and Robert D.\ Skeel},
  title = {Nonlinear instability in multiple time stepping molecular dynamics},
  booktitle = {Proceedings of the {ACM} Symposium on Applied Computing ({SAC} 03),
	Melbourne, {F}l},
  year = {2003},
  pages = {167--171},
  address = {Melbourne, Florida},
  month = MAR,
  publisher = {ACM Press}
}

@UNPUBLISHED{KoIz0x,
  author = {Alice Ko and Jes{\'u}s A. Izaguirre},
  title = {MDSimAid: Automatic Optimization of Fast Electrostatic Algorithms
	for Molecular Simulations},
  note = {SIAM Conference on Computational Science and Engineering, CSE 2003.
	Preprint at \texttt{http://www.nd.edu/\~{ }izaguirr/papers/mdsimaid.pdf}},
  month = FEB,
  year = {2003},
  address = {San Diego, CA}
}

@INPROCEEDINGS{AKGJ03,
  author = {M. S. Alber and M. A. Kiskowski and J. A. Glazier and Y. Jiang},
  title = {On cellular automaton approaches to modeling biological cells},
  booktitle = {IMA Mathematical Systems Theory in Biology, Communication, and Finance},
  year = {2003},
  editor = {J. Rosenthal and D. S. Gilliam},
  volume = {134},
  pages = {1--39},
  publisher = {Springer-Verlag, New York}
}

@MISC{APAC03,
  author = {Apache},
  title = {Xerces {C}++ Parser},
  howpublished = {\url{http://xml.apache.org/xerces-c/index.html}},
  year = {2003},
  annote = {Xerces Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{ROSE,
  author = {David Baker},
  title = {Rosetta@home},
  school = {University of Washington},
  note = {{\small \texttt{http://boinc.bakerlab.org/rosetta}}}
}

@ARTICLE{Asip03,
  author = {M.~Asipauskas and M.~Aubouy and J.~A. Glazier and F.~Graner and Y.~Jiang},
  title = {A texture tensor to quantify deformations: the example of two-dimensional
	flowing foams},
  journal = {Granular Matter},
  year = {2003},
  volume = {5},
  pages = {71--74},
  number = {2}
}

@PHDTHESIS{Blik03,
  author = {Ragnhild Blikberg},
  title = {Nested Parallelism in OpenMP with Application to Adaptive Mesh Refinement},
  school = {University of Bergen},
  year = {2003},
  address = {Bergen, Norway}
}

@ARTICLE{BoOs03,
  author = {P. Bode and J. P. Ostriker},
  title = {Tree-{P}article {M}esh: An Adaptive, Efficient, and Parallel Code
	for Collisionless Cosmological Simulation},
  journal = {Astrophysical J. Supplement Series},
  year = {2003},
  volume = {145},
  pages = {1--13},
  number = {1}
}

@ARTICLE{Bolh03,
  author = {P.~Bolhuis},
  title = {Transition path sampling of ${\beta}$-hairpin peptide},
  journal = PNAS,
  year = {2003},
  volume = {100},
  pages = {12129-12134},
  number = {21}
}

@ARTICLE{CarE03,
  author = {A.~E.~Cardenas and R.~Elber},
  title = {Kinetics of cytochrome {C} folding:Atomically detailed simulations},
  journal = PRO,
  year = {2003},
  volume = {51},
  pages = {245-257}
}

@ARTICLE{CarE03a,
  author = {A.~E.~Cardenas and R.~Elber},
  title = {Atomically detailed simulations of helix formation with the stochastic
	difference equation},
  journal = BJ,
  year = {2003},
  volume = {85},
  pages = {2919-2939}
}

@INCOLLECTION{CHAT03,
  author = {R.\ Chaturvedi and J.~A.\ Izaguirre and C.\ Huang and T.\ Cickovski
	and P.\ Virtue and G.\ Thomas and G.\ Forgacs and M.~S.\ Alber and
	H.~G.~E.\ Hentschel and S.~A.\ Newman and J.~A.\ Glazier},
  title = {Multi-model simulations of chicken limb morphogenesis},
  booktitle = {Lecture Notes in Computational Science},
  publisher = {Springer-Verlag, Berlin},
  year = {2003},
  volume = {2659},
  pages = {39--49}
}

@MISC{Coff03,
  author = {J. Coffland},
  title = {BasicUtils},
  howpublished = {\url{http://compucell.sourceforge.net/phpwiki/index.php/BasicUtils}},
  year = {2003},
  annote = {BasicUtils home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{Coff03a,
  author = {Joseph Coffland},
  title = {XMLCereal Libraries},
  howpublished = {\url{http://sourceforge.net/projects/xmlcereal}},
  year = {2003},
  annote = {XMLCereal home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@MISC{Coff03b,
  author = {Joseph Coffland},
  title = {prtpacker - Portable Resource Tree Packer},
  howpublished = {\url{http://prtpacker.sourceforge.net}},
  year = {2003},
  annote = {prtpacker home page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@BOOK{DeDN03,
  title = {Object-Oriented Reengineering Patterns},
  publisher = {Morgan Kauffman},
  year = {2003},
  author = {S. Demeyer and S. Ducasse and O. Nierstrasz}
}

@ARTICLE{DoEi03,
  author = {Jack Dongarra and Victor Eijkhout},
  title = {Self-adapting Numerical Software for Next Generation Applications},
  journal = IJHPCA,
  year = {2003},
  volume = {17},
  pages = {125--131},
  number = {2},
  nremark = {A recommender example}
}

@ARTICLE{DuFS03,
  author = {D.~Duguay and R.~A. Foty and M.~S. Steinberg},
  title = {Cadherin-mediated cell adhesion and tissue segregation: qualitative
	and quantitative determinants},
  journal = {Dev. Biol.},
  year = {2003},
  volume = {253},
  pages = {309--323},
  number = {2}
}

@ARTICLE{EGCS03,
  author = {R.~Elber and A.~Ghosh and A.~Cardenas and H.~Stern},
  title = {Bridging the gap between reaction pathways, long time dynamics and
	calculation of rates},
  journal = ACP,
  year = {2003},
  volume = {126},
  pages = {93-129}
}

@ARTICLE{EMWT03,
  author = {E.~M.~Emberly and R.~Mukhopadhyay and N.~S.~Wingreen and C.~Tang},
  title = {Flexibility of ${\alpha}$-Helices: Results of a Statistical Analysis
	of Database of Protein Structures},
  journal = JMB,
  year = {2003},
  volume = {327},
  pages = {229--237}
}

@MASTERSTHESIS{Engl03,
  author = {R. D. Engle},
  title = {Interpolated Modified {H}amiltonians},
  school = {Department of Computer Science, University of Illinois},
  year = {2003},
  address = {Urbana-Champaign, USA}
}

@ARTICLE{faller03:_errat,
  author = {Roland Faller and Juan J. de Pablo},
  title = {Erraturm: "Constant Pressure Hybrid Molecular Dynamics---{M}onte
	{C}arlo Simulations" [J. Chem. Phys. 116, 55 (2002)]},
  journal = JCP,
  year = {2003},
  volume = {119},
  pages = {7605},
  number = {14}
}

@PHDTHESIS{Fisc03,
  author = {Alexander Fischer},
  title = {An uncoupling-coupling method for {M}arkov chain {M}onte {C}arlo
	simulations with an application to biomolecules},
  school = {Freie Universitat Berlin},
  year = {2003},
  address = {Berlin, Germany}
}

@ARTICLE{GFC+03,
  author = {A. Gamba and D. Ambrosi and A. Coniglio and A. DeCandia and S. DiTalia
	and E. Giraudo and G. Serini and L. Preziosi and F. Bussolino},
  title = {Percolation morphogenesis and {B}urgers dynamics in blood vessels
	formation},
  journal = PRL,
  year = {2003},
  volume = {90},
  pages = {118101}
}

@ARTICLE{GaCh03,
  author = {C. K. Gan and M. Challacombe},
  title = {Linear Scaling Computation of the {F}ock Matrix. VI. {D}ata Parallel
	Computation of the Exchange-Correlation Matrix},
  journal = JCP,
  year = {2003},
  volume = {118},
  pages = {9128--9135},
  number = {20}
}

@ARTICLE{GGF+03,
  author = {H. Gerhardt and M. Golding and M. Fruttiger and C. Ruhrberg and A.
	Lundkvist and A. Abramsson and M. Jeltsch and C. Mitchell and K.
	Alitalo and D. Shima and C. Betsholtz},
  title = {Vegf guides angiogenic sprouting utilizing endothelial tip cell filopodia},
  journal = {J. Cell Biol.},
  year = {2003},
  volume = {161},
  pages = {1163--1177},
  annote = {Vascular endothelial growth factor (VEGF-A) is a major regulator
	of blood vessel formation and function. it controls several processes
	in endothelial cells such as proliferation survival and migration
	but it is not known how these are coordinately regulated to result
	in more complex morphogenetic events such as tubular sprouting fusion
	and network formation. We show here that VEGF-A controls angiogenic
	sprouting in the early postnatal retina by guiding filopodial extension
	from specialized endothelial cells situated at the tips of the vascular
	sprouts. The tip cells respond to VEGF-A only by guided migration;
	the proliferative response to VEGF-A occurs in the sprout stalks.
	These two cellular responses are both mediated by agonistic activity
	of VEGF-A on VEGF receptor 2. Whereas tip cell migration depends
	on a gradient of VEGF-A proliferation is regulated by its concentration.
	Thus vessel patterning during retinal angiogenesis depends on the
	balance between two different qualities of the extracellular VEGF-A
	distribution which regulate distinct cellular responses in defined
	populations of endothelial cells. PY 2003},
  from = {INSTITUTE OF SCIENTIFIC INFORMATION:}
}

@BOOK{GILB03,
  title = {Developmental Biology, Seventh Edition},
  publisher = {Sinauer Associates},
  year = {2003},
  author = {S. F. Gilbert},
  address = {Sunderland, MA}
}

@ARTICLE{GrWP03,
  author = {Michael J. Grey and Chunyu Wang and Arthur G. Palmer III},
  title = {Disulfide Bond Isomerization in Basic Pancreatic Trypsin Inhibitor:
	Multisite Chemical Exchange Quantified by CPMG Relaxation Dispersion
	and Chemical Shift Modeling},
  journal = JACS,
  year = {2003},
  volume = {125},
  pages = {14324--14335}
}

@ARTICLE{Groo03,
  author = {R. D. Groot},
  title = {Electrostatic Interactions in Dissipative Particle Dynamics-Simulation
	of Polyelectrolytes and Anionic Surfactants},
  journal = JCP,
  year = {2003},
  volume = {118},
  pages = {11265--11277},
  number = {24},
  abstract = {Electrostatic interactions have been incorporated in dissipative particle
	dynamics (DPD) simulation. The electrostatic field is solved locally
	on a grid. Within this formalism, local inhomogeneities in the electrostatic
	permittivity can be treated without any problem. Key issues like
	the screening of the potential near a charged surface and the Stillinger-Lovett
	moment conditions are satisfied. This implies that the method captures
	the essential features of electrostatic interaction. For the direct
	simulation of mixed surfactants near oil-water interfaces, or for
	the simulation of Coulombic polymer-surfactant interactions, this
	method has all the advantages of DPD over full atomistic molecular
	dynamics (MD). DPD has proven to be faster than MD by many orders
	of magnitude, depending on the precise scaling factor chosen for
	the simulation. This brings phenomena of microseconds in reach of
	routine simulation, while maintaining a fairly accurate representation
	of the structure of the molecules. As an example of this simulation
	tool, the interaction between a cationic polyelectrolyte and anionic
	surfactant is discussed. Without a surfactant, the polyelectrolyte
	shows a fractal dimensionality that is in line with the theoretical
	and experimental values cited in literature, it behaves as a fairly
	stiff rod, d(f)similar to1.1. When salt is replaced by anionic surfactant,
	the polymer wraps around one or more discrete surfactant micelles,
	in line with the current understanding of these systems, and scaling
	invariance in the correlation function is broken.}
}

@PHDTHESIS{Habe03,
  author = {P. Habegger},
  title = {Evaluating Internet Topologies: An Assessment and a Framework},
  school = {Institute of Computer Science and Applied Mathematics, University
	of Berne},
  year = {2003}
}

@ARTICLE{HBOG03,
  author = {W. Miachel Hanson and Scott A. Beeser and Terrence G. Oas and David
	P. Goldenberg},
  title = {Identification of a Residue Critical for Maintaining the Functional
	Conformation of BPTI},
  journal = JMB,
  year = {2003},
  volume = {333},
  pages = {425--441}
}

@ARTICLE{HaDB03,
  author = {D. J. Harvey and S. K. Das and R. Biswas},
  title = {Designing an Efficient Partitioning Algorithm for Grid Environments
	with Application to n-Body Problems},
  journal = ICCSA,
  year = {2003},
  volume = {2668},
  pages = {279--289},
  nremark = {Runtime load balancing for the grid}
}

@ARTICLE{HuKe03,
  author = {G. Hummer and I.~G. Kevrekidis},
  title = {Coarse molecular dynamics of a peptide fragment: {F}ree energy, kinetics
	and long-time dynamics computation },
  journal = JCP,
  year = {2003},
  volume = {118},
  pages = {10762--10773}
}

@ARTICLE{KuFe03,
  author = {S. P. Kumar and J. C. Feidler},
  title = {BioSPICE, 2},
  journal = {Omics: A Journal of Integrative Biology},
  year = {2003},
  volume = {7},
  pages = {335},
  number = {4}
}

@ARTICLE{LaPN03,
  author = {K. A. Landman and G. J. Pettet and D. F. Newgreen},
  title = {Mathematical models of cell colonization of uniformly growing domains},
  journal = {Bull. Math. Biol.},
  year = {2003},
  volume = {65},
  pages = {235--262},
  number = {2}
}

@ARTICLE{LMOW03,
  author = {A. Lew and J.\ E.\ Marsden and M.\ Ortiz and M.\ West},
  title = {Asynchronous Variational Integrators},
  journal = {Arch. Ration. Mech. Anal.},
  year = {2003},
  volume = {167},
  pages = {85--146}
}

@ARTICLE{LiHH03,
  author = {Chai-Yu Lin and Chin-Kun Hu and Ulrich H. E. Hansmann},
  title = {Parallel Tempering Simulations of HP-36},
  journal = {PROTEINS:Structure,Function, and Genetics},
  year = {2003},
  volume = {52},
  pages = {436--445}
}

@MISC{Lua03,
  author = {Lua},
  title = {Lua, The Programming Language},
  year = {2003},
  note = {\url{http://www.lua.org}}
}

@PHDTHESIS{Ma2003,
  author = {Q. Ma},
  title = {Novel Multiscale Algorithms for Molecular Dynamics},
  school = {University of Notre Dame},
  year = {2003},
  address = {Notre Dame, Indiana, USA}
}

@ARTICLE{MaIz03a,
  author = {Q.\ Ma and J.~A.\ Izaguirre},
  title = {Targeted Mollified Impulse --- a Multiscale Stochastic Integrator
	for Long Molecular Dynamics Simulations},
  journal = MMS,
  year = {2003},
  volume = {2},
  pages = {1--21},
  number = {1}
}

@INPROCEEDINGS{MaIz03b,
  author = {Q. Ma and J.~A. Izaguirre},
  title = {Long time step molecular dynamics using targeted Langevin stabilization},
  booktitle = {Proceedings of the {ACM} Symposium on Applied Computing ({SAC} 03),
	{M}elbourne, {FL}},
  year = {2003},
  pages = {178--182},
  address = {New York},
  publisher = {ACM}
}

@INPROCEEDINGS{MaIz0xa,
  author = {Q. Ma and J.~A. Izaguirre},
  title = {Targeted Langevin stabilization of molecular dynamics},
  booktitle = {Proc. of the \emph{SIAM Conference on Computational Science and Engineering
	(CSE'03)}(CD-ROM)},
  year = {2003},
  address = {San Diego, CA},
  publisher = SJSSC
}

@ARTICLE{MaIS03,
  author = {Q.\ Ma and J.~A.\ Izaguirre and R.~D.\ Skeel},
  title = {{V}erlet-{I}/r-{RESPA}/{I}mpulse is limited by nonlinear instability},
  journal = SJSC,
  year = {2003},
  volume = {24},
  pages = {1951--1973},
  number = {6}
}

@ARTICLE{MaHD03,
  author = {T. Matthey and J.~P. Hansen and M. Drewsen},
  title = {Coulomb bi-crystals of species with identical charge-to-mass ratios},
  journal = PRL,
  year = {2003},
  volume = {91},
  pages = {165001},
  number = {16}
}

@INCOLLECTION{MaKI03,
  author = {T. Matthey and A. Ko and J.~A. Izaguirre},
  title = {{P}roto{M}ol, an object-oriented framework for algorithmic development},
  booktitle = {Computational Science---{ICCS} 2003, International Conference, Melbourne,
	Australia and St. Petersburg, Russia},
  publisher = {Springer-Verlag},
  year = {2003},
  pages = {50--59},
  address = {Berlin},
  note = {Lecture {N}otes {C}omputational {S}cience 2659.}
}

@ARTICLE{MiSO03,
  author = {Ayori Mitsutake and Yuji Sugita and Yuko Okamoto},
  title = {Replica-exchange multicanonical and multicanonical replica-exchange
	{M}onte {C}arlo simulations of peptides. {F}ormulation and benchmark
	test},
  journal = JCP,
  year = {2003},
  volume = {118},
  pages = {6664--6675},
  number = {14}
}

@ARTICLE{OGR+03,
  author = {W.~B.~Ouchi and J.~A. Glazier and J.~P. Rieu and A.~Upadhyaya and
	Y.~Sawada},
  title = {Improving the realism of the cellular Potts model in simulation of
	biological cells},
  journal = {Physica A},
  year = {2003},
  volume = {329},
  pages = {451--458},
  number = {3--4}
}

@ARTICLE{PLIM03,
  author = {S. J. Plimpton and D. B. Seidel and M. F. Pasik and R. S. Coats and
	G. R. Montry},
  title = {A Load-Balancing Algorithm For A Parallel Electromagnetic Particle-In-Cell
	Code},
  journal = CPC,
  year = {2003},
  volume = {152},
  pages = {227--241},
  number = {2}
}

@ARTICLE{ReJi03,
  author = {N. Reuter and K. Hinsen et al.},
  title = {Transconformations of the SERCA1 Ca-ATPase: a normal mode study},
  journal = {Biophys. J.},
  year = {2003},
  volume = {85},
  pages = {2186--97},
  number = {4}
}

@ARTICLE{RhPa03,
  author = {Young Min Rhee and Vijay S. Pande},
  title = {Multiplexed-Replica Exchange Molecular Dynamics Method for Protein
	Folding Simulation},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {84},
  pages = {775--786}
}

@ARTICLE{SAG+03,
  author = {G. Serini and D. Ambrosi and E. Giraudo and A. Gamba and L. Preziosi
	and F. Bussolino},
  title = {Modeling the early stages of vascular network assembly},
  journal = {Embo. J.},
  year = {2003},
  volume = {22},
  pages = {1771--1779}
}

@MISC{Spir03,
  author = {SPIRAL},
  title = {Software/Hardware Generation for DSP Algorithms},
  howpublished = {\url{http://www.spiral.net}},
  year = {2003},
  annote = {SPIRAL Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{StBB03,
  author = {M.~A. Stijnman and R.~H. Bisseling and G.~T. Barkema},
  title = {Partitioning 3D space for parallel many-particle simulations},
  journal = {Computer Physics Communications},
  year = {2003},
  volume = {149},
  pages = {121--134},
  number = {3}
}

@ARTICLE{TaIS03,
  author = {K. Takahashi and N. Ishikawa and Y. Sadamoto and S. Ohta and A. Shiozawa
	and F. Miyoshi and Y. Naito and Y. Nakayama and M. Tomita},
  title = {{E}-{CELL}2: Multi-platform {E}-{CELL} simulation system},
  journal = {Bioinformatics},
  year = {2003},
  volume = {19},
  pages = {1727--1729}
}

@ARTICLE{VaDo03,
  author = {Sathish S. Vadhiyar and Jack J. Dongarra},
  title = {Self Adaptivity in Grid Computing},
  journal = CPE,
  year = {2003},
  nremark = {A recommender example.}
}

@ARTICLE{ZaJG03,
  author = {M.~Zajac and G.~L. Jones and J.~A. Glazier},
  title = {Simulating convergent extension by way of anisotropic differential
	adhesion},
  journal = {J.\ Theor.\ Biol.},
  year = {2003},
  volume = {222},
  pages = {247--259},
  number = {2}
}

@MASTERSTHESIS{Ko2002,
  author = {Alice Ko},
  title = {{MDSimAid}: An Automatic Recommender for Optimization of Fast Electrostatic
	Algorithms for Molecular Simulations},
  school = {University of Notre Dame},
  year = {2002},
  address = {Notre Dame, Indiana, USA},
  month = DEC,
  annote = {Available from \texttt{http://www.nd.edu/\~{ }izaguirr/papers/KOthesis.pdf}}
}

@UNPUBLISHED{Skee02,
  author = {Robert D. Skeel},
  title = {Why Does Molecular Dynamics Work},
  note = {Presented in CIMMS-IPAM Workshop -- Molecular Modeling and Computation:
	Perspectives and Challenges},
  month = NOV,
  year = {2002},
  annote = {Abstract: First, it is acknowledged that a number of scientists do
	not believe that molecular dynamics does work, including some who
	accept the validity of molecular mechanics. Second, this presentation
	does not address the accuracy of classical force fields as an approximation
	to quantum mechanics, nor is it primarily concerned with defects
	in the ergodic hypothesis. Rather, the concern is that computed trajectories
	are overwhelmed by the effect of finite step size (and finite precision)
	due to the chaotic nature of the {H}amiltonian systems and the very
	long integration times. The best-behaved numerical simulations are
	generally those that employ symplectic integrators. For these it
	can be proved that the numerical solution is very nearly the exact
	solution of a modified {H}amiltonian system on a limited time interval.
	However, from examining the numerical trajectories of one-dimentional
	systems, it is not apparent that this result extends to very lon!
	g time intervals. The aim of the presentation is to give a plausible
	mathematical basis for long time numerical integration using the
	concept of weak convergence.}
}

@TECHREPORT{AKGJ02,
  author = {Mark S. Alber and Maria A. Kiskowski and James A. Glazier and Yi
	Jiang},
  title = {On cellular automaton approaches to modeling biological cells},
  institution = {University of Notre Dame},
  year = {2002},
  number = {337},
  address = {Department of Mathematics},
  month = SEP
}

@ARTICLE{Rapa02,
  author = {D.~C. Rapaport},
  title = {Molecular dynamics simulation of polymer helix formation using rigid-link
	methods},
  journal = PRE,
  year = {2002},
  pages = {11906},
  month = {Jul}
}

@TECHREPORT{HaRe02,
  author = {B. Hafskjold and L. Rekvig},
  title = {Comparison between \textsc{ProtoMol} and {NEMD} for a simple {L}ennard-{J}ones
	system},
  institution = {Department of Chemistry, Trondheim, {NTNU}},
  year = {2002},
  month = MAR
}

@ARTICLE{Akke02,
  author = {Mikael Akke},
  title = {{NMR} methods for characterizing microsecond to millisecond dynamics
	in recognition and catalysis},
  journal = {Current Opinion in Structural Biology},
  year = {2002},
  volume = {12},
  pages = {642--647}
}

@ARTICLE{ArCl02,
  author = {B. W. Arbuckle and P. Clancy},
  title = {Effects of the {E}wald sum on the free energy of the extended simple
	point charge model for water},
  journal = JCP,
  year = {2002},
  volume = {116},
  pages = {5090--5098},
  number = {12},
  annote = {The effects of including the Ewald sum on several key system properties
	for the extended simple point charge (SPC/E) model of water, in the
	temperature range of 140-300 K have been investigated using molecular
	dynamics simulations. The original SPC/E parameters are used without
	alteration since this study is intended to determine whether the
	Ewald sum affects the model sufficiently to warrant reparameterization.
	Overall comparison to experiment has been improved for the liquid
	phase as evidenced by several factors. The effect of temperature
	on the self-diffusivity coefficient has improved in the range from
	300 to 200 K. There is a shift in the temperature at which the density
	maximum occurs (260 K from 255 K in previous simulations of SPC/E
	water without the Ewald) and the value of max has decreased to 1.0003
	g/ml (versus 0.99997 g/ml for experiment at 277 K) from 1.0082 g/ml
	for the SPC/E model. However, the shape of the (T) profile is worse
	than without the Ewald sum in comparison to experiment, but is qualitatively
	similar to {M}onte {C}arlo data from Harrington et al. for SPC/E
	modeled water including a reaction field method. For the solid, while
	the (T) profile is unchanged, values are worse than without an Ewald
	sum in comparison to experiment (3\% higher than experiment without
	the Ewald and 5\% with the Ewald). Calculation of free energies of
	various low pressure ices and liquid water using thermodynamic integration
	has produced the major finding, the determination of a melting point
	for low pressure ices. The melting points of proton-disordered ices
	Ih and Ic were found to be 279+/-5 K and 291+/-5 K, respectively.
	Melting points of their proton-ordered counterparts are 284+/-5 K
	(Ih) and 281+/-5 K (Ic)}
}

@INPROCEEDINGS{BaLR02,
  author = {E. Barth and B. Leimkuhler and Sebastian Reich},
  title = {A Test Set for Molecular Dynamics Algorithms},
  booktitle = {Computational Methods for Macromolecules: Challenges and Applications},
  year = {2002},
  editor = {T.J. Barth and M. Griebel and D.E. Keyes and R.M. Nieminen and D.
	Roose and T. Schlick},
  volume = {24},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {73--103},
  publisher = {Springer}
}

@ARTICLE{BBC+02,
  author = {G. Baurngartner and D. E. Bernholdt and D. Cociorva and R. Harrison
	and S. Hirata and C. C. Larn and M. Nooijen and R. Pitzer and J.
	Ramanujam and P. Sadayappan},
  title = {A High-Level Appropach to Synthesis of High-Performance Codes for
	Quantum Chemistry},
  journal = {Proceedings of Supercomputing~'02},
  year = {2002}
}

@ARTICLE{BBPL91,
  author = {Baschnagel J. and K. Binder and W. Paul and M. Laso and U. Suter and I. Batoulis and W. Jilge and T. Burger},
  title = {On the Construction of Coarse-Grained Models for Linear Flexible Polymer-Chains - Distribution-Functions for Groups of Consecutive Monomers},
  journal = JCP,
  volume = {95},
  pages = {6014--6025},
  year = {1991}
}


@ARTICLE{Blil02,
  author = {C. Blilie},
  title = {Patterns in scientific software; An introduction},
  journal = {Computing in Science and Engineering},
  year = {2002},
  volume = {4},
  pages = {48--53},
  number = {3}
}

@ARTICLE{BCDG02,
  author = {P.~G.~Bolhuis and D.~Chandler and C.~Dellago and P.~L.~Geissler},
  title = {Transition Path Sampling: Throwing ropes over rough mountain passes,
	in the dark},
  journal = ARBBC,
  year = {2002},
  volume = {53},
  pages = {291--318}
}

@ARTICLE{Carl02,
  author = {Heather A. Carlson},
  title = {Protein flexibility and drug design: how to hit a moving target},
  journal = COCHB,
  year = {2002},
  volume = {6},
  pages = {447--452},
  number = {4},
  url = {http://www.sciencedirect.com/science/article/B6VRX-465S0S4-1/2/e4f672e9c702533b135b98411df58b9a}
}

@ARTICLE{CrHM02,
  author = {E. J. Crampin and W. W. Hackborn and P. K. Maini},
  title = {Pattern formation in reaction-diffusion models with nonuniform domain
	growth},
  journal = {Bull. Math. Biol.},
  year = {2002},
  volume = {64},
  pages = {747--769},
  number = {4}
}

@MISC{DARP02,
  author = {DARPA},
  title = {DARPA News Release: {\em DARPA Releases BioSPICE Software}},
  year = {2002},
  note = {\url{https://community.biospice.org/public/bio_release.pdf}}
}

@ARTICLE{Dav+02,
  author = {E.H. Davidson and J. P. Rast and P. Oliveri and A. Ransick and C.
	Calestani and C.H. Yuh and T. Minokawa and G. Amore and V. Hinman
	and C.Arenas-Mena and O. Otim and C.T. Brown and C.B. Livi and P.Y.
	Lee and R. Revilla and A.G. Rust and Z. Pan and M.M. Schilstra and
	P.J.C. Clarke and M.I. Arnone and L. Rowen and R.A. Cameron and D.R.
	McClay and L. Hood and H. Bolouri},
  title = {A Genomic Regulatory Network for Development},
  journal = SCI,
  year = {2002},
  volume = {295},
  pages = {1669}
}

@ARTICLE{DaWP02,
  author = {Eric Darve and Michael A. Wilson and Andrew Pohorille},
  title = {Calculating Free Energies Using a Scaled-Force Molecular Dynamics Algorithm},
  journal = {Molecular Simulation},
  year = {2002},
  volume = {28},
  pages = {113}
}

@ARTICLE{DEHN02,
  author = {W. Dehnen},
  title = {A Hierarchical {O(N)} Force Calculation Algorithm},
  journal = JCP,
  year = {2002},
  volume = {179},
  pages = {27--42},
  number = {1}
}

@ARTICLE{DeBG02,
  author = {C. Dellago and P.~G.Bolhuis and P.~L. Geissler},
  title = {Transition Path Sampling},
  journal = ACP,
  year = {2002},
  number = {123}
}

@ARTICLE{FaDe02,
  author = {Roland Faller and Juan J. de Pablo},
  title = {Constant Pressure Hybrid {M}olecular {D}ynamics---{M}onte {C}arlo
	Simulations},
  journal = JCP,
  year = {2002},
  volume = {116},
  pages = {55--59},
  abstract = {New hybrid Molecular Dynamics {M}onte {C}arlo methods are proposed
	to increase the efficiency ofconstant-pressure simulations. Two variations
	of the isobaric Molecular Dynamics component of thealgorithms are
	considered. In the first, we use the extended-ensemble method of
	Andersen (H. C.Andersen, J. Chem. Phys. 72, 2384 ~1980). In the second,
	we arrive at a new constant-pressure {M}onte {C}arlo technique based
	on the reversible generalization of the weak-coupling barostat (H.
	J.C. Berendsen et al., J. Chem. Phys. 81, 3684 ~1984). This latter
	technique turns out to be highlyeffective in equilibrating and maintaining
	a target pressure. It is superior to the extended-ensemblemethod,
	which in turn is superior to simple volume-rescaling algorithms.
	The efficiency of theproposed methods is demonstrated by studying
	two systems. The first is a simple Lennard-Jonesfluid. The second
	is a mixture of polyethylene chains of 200 monomers.}
}

@ARTICLE{FaPa02,
  author = {Roland Faller and Juan J. de Pablo},
  title = {Constant pressure hybrid Molecular Dynamics -- {M}onte {C}arlo simulations},
  journal = JCP,
  year = {2002},
  volume = {116},
  pages = {55--59},
  number = {1}
}

@BOOK{FLAN02,
  title = {Java in a Nutshell: Fourth Edition},
  publisher = {O'Reilley},
  year = {2002},
  author = {D. Flanigan}
}

@BOOK{FOWL02,
  title = {Patterns of Enterprise Application Architecture},
  publisher = {Addison-Wesley},
  year = {2002},
  author = {M. Fowler},
  address = {Boston}
}

@BOOK{FrSm02,
  title = {Understanding Molecular Simulation},
  publisher = {Academic Press},
  year = {2002},
  author = {Daan Frenkel and Berend Smit},
  address = {San Diego},
  edition = {2nd}
}

@PHDTHESIS{Gill02,
  author = {Malcolm Bjorn Gillies},
  title = {Computational studies of protein-ligand molecular recognition},
  school = {Utrecht University},
  year = {2002}
}

@TECHREPORT{GMPR02,
  author = {G. Gupta and B. Milligan and E. Pontelli and D. Ranjan},
  title = {Logic Programming and Domain Specific Languages: A Case Study For
	Phylogenetic Inference Problems},
  institution = {Departament of Computer Science},
  year = {2002},
  number = {2002/4},
  address = {University of Texas}
}

@BOOK{HaLW02,
  title = {Geometric Numerical Integration: Structure-Preserving Algorithms
	for Ordinary Differential Equations},
  publisher = {Springer-Verlag},
  year = {2002},
  author = {Ernst Hairer and Christian Lubich and Gerhard Wanner},
  volume = {31},
  series = {Springer Series in Computational Mathematics},
  address = {Berlin}
}

@BOOK{Heat02,
  title = {Scientific Computing: An Introductory Survey},
  publisher = {McGraw Hill},
  year = {2002},
  author = {Michael~T. Heath},
  edition = {2nd}
}

@BOOK{Held02,
  title = {Imaginal Discs: The Genetic and Cellular Logic of Pattern Formation},
  publisher = {Cambridge University Press},
  year = {2002},
  author = {L. I. Held},
  address = {New York}
}

@UNPUBLISHED{HTNG02,
  author = {H.G.E. Hentschel and t. Glimm and S.A. Newman and J.A. Glazier},
  title = {Mechanisms of cell condensation in early avian limb development},
  note = {preprint submitted to Elsevier preprint},
  year = {2002}
}

@ARTICLE{Hoge02,
  author = {P.~Hogeweg},
  title = {Computing an organism: on the interface between informatic and dynamic
	processes},
  journal = {Biosystems},
  year = {2002},
  volume = {64},
  pages = {97--109},
  number = {1--3},
  nremark = {Sp. Iss. SI Jan 2002}
}

@ARTICLE{Hous02,
  author = {Elias~N. Houstis and Ann Christine Catlin and John R. Rice and Naren
	Ramakrishnan and Vassilios S. Verykios},
  title = {{M}y{PYTHIA}: A Recommendation Portal for Scientific Software and
	Services},
  journal = {Concurrency and Computation: Practice and Experience},
  year = {2002},
  volume = {14},
  pages = {1481--1505},
  number = {13--14},
  nremark = {A recommender example.}
}

@MISC{ICSB02,
  author = {ICSB},
  title = {Interdisciplinary Center for the Study of Biocomplexity},
  howpublished = {{\tt \small http://www.nd.edu/\~{}icsb}},
  year = {2002},
  note = {Homepage for the ICSB at the University of Notre Dame}
}

@INCOLLECTION{IMM+01b,
  author = {J.~A. Izaguirre and Q. Ma and T. Matthey and J. Willcock and T. Slabach
	and B. Moore and G. Viamontes},
  title = {Overcoming Instabilities in {V}erlet-{I}/{r}-{RESPA} with the Mollified
	Impulse Method},
  booktitle = {Proceedings of 3rd International Workshop on {M}ethods for {M}acromolecular
	{M}odeling},
  publisher = {Springer-Verlag},
  year = {2002},
  editor = {T. Schlick and H.~H. Gan},
  volume = {24},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {146--174},
  address = {New York},
  annote = {Preprint: \url{http://www.nd.edu/\~izaguirr/papers/newM3paper.pdf}}
}

@INCOLLECTION{IMM+02,
  author = {J.~A. Izaguirre and Q. Ma and T. Matthey and J. Willcock and T. Slabach
	and B. Moore and G. Viamontes},
  title = {Overcoming Instabilities in {V}erlet-{I}/{r}-{RESPA} with the Mollified
	Impulse Method},
  booktitle = {Proceedings of the 3rd International Workshop on {M}ethods for {M}acromolecular
	{M}odeling},
  publisher = {Springer-Verlag, Berlin},
  year = {2002},
  editor = {T. Schlick and H.~H. Gan},
  volume = {24},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {146--174},
  address = {New York}
}

@INPROCEEDINGS{John02,
  author = {David S. Johnson},
  title = {A Theoretician's Guide to the Experimental Analysis of Algorithms},
  booktitle = {Data Structures, Near Neighbor Searches, and Methodology: Fifth and
	Sixth DIMACS Implementation Challenges},
  year = {2002},
  editor = {M. Goldwasser and D. S. Johnson and C. C. McGeoch},
  pages = {215--250},
  address = {Providence, RI},
  publisher = AMS
}

@BOOK{Jeff97,
  title = {An Introduction to Hydrogen Bonding},
  publisher = {Oxford University Press},
  year = {1997},
  author = {George A. Jeffery},
  series = {Topics in Physical Chemistry},
  address = {USA},
  isbn = {0195095480}
}

@ARTICLE{deJo02,
  author = {H. De Jong},
  title = {Modeling and Simulation of Genetic Regulatory Systems: A Literature
	Review},
  journal = {J. Comp. Biol.},
  year = {2002},
  volume = {9},
  pages = {69--105},
  number = {1}
}

@ARTICLE{Kofk02,
  author = {D. A. Kofke},
  title = {On the acceptance probability of replica-exchange {M}onte {C}arlo
	trials},
  journal = JCP,
  year = {2002},
  volume = {117},
  pages = {6911}
}

@PHDTHESIS{Matt02,
  author = {Thierry Matthey},
  title = {Framework Design, Parallelization and Force Computation in Molecular
	Dynamics},
  school = {University of Bergen},
  year = {2002},
  address = {Bergen, Norway}
}

@ARTICLE{MDB+02,
  author = {M. Z. Moftah and S. A. Downie and N. B. Bronstein and N. Mezentseva
	and J. Pu and P. A. Maher and S. A. Newman},
  title = {Ectodermal {FGF}s Induce Perinodular Inhibition of Limb Chondrogenesis
	In Vitro and In Vivo Via {FGF} Receptor 2},
  journal = {Dev. Biol.},
  year = {2002},
  volume = {249},
  pages = {270--282},
  number = {2}
}

@ARTICLE{MoEd02,
  author = {A.~Mogilner and L.~Edelstein-Keshet},
  title = {Regulation of actin dynamics in rapidly moving cells: A quantitative
	analysis},
  journal = {Biophys. J},
  year = {2002},
  volume = {83},
  pages = {1237--1258},
  number = {3}
}

@ARTICLE{OnCB02,
  author = {A.~Onufriev and D.~A.~Case and A.~Bashford},
  title = {Effective Born radii in the generalized born approximation:The importance
	of being perfect},
  journal = JCC,
  year = {2002},
  volume = {23},
  pages = {1297-1304},
  number = {14}
}

@ARTICLE{OMSO02,
  author = {Fredrik Osterberg and Garrett M. Morris and Michel F. Sanner and
	Arther J. Olson and David S. Goodsell},
  title = {Automated Docking to Multiple Target Structures: Incorporatin of
	Protein Mobility and Structural Water Heterogeneity in AutoDock},
  journal = PRO,
  year = {2002},
  volume = {46},
  pages = {34--40}
}

@ARTICLE{Raey02,
  author = {L. Raeymaekers},
  title = {Dynamics of {B}oolean networks controlled by biologically meaningful
	functions},
  journal = {J. Theor. Biol.},
  year = {2002},
  volume = {218},
  pages = {331--341},
  number = {3}
}

@ARTICLE{SaGa02,
  author = {K. Sanbonmatsu and A. E. Garcia},
  title = {Structure of Met-enkephalin in explicit aqueous solution using replica
	exchange molecular dynamics},
  journal = {Proteins:Struct.,Funct,Genet.},
  year = {2002},
  volume = {46},
  pages = {225}
}

@BOOK{Schl02,
  title = {Molecular Modeling and Simulation - An Interdisciplinary Guide},
  publisher = {Springer-Verlag},
  year = {2002},
  author = {Tamar Schlick},
  address = {New York, NY},
  remark = {ISBN: 0-387-95404-X}
}

@BOOK{ShTr02,
  title = {Design Patterns Explained: A New Perspective on Object-Oriented Design},
  publisher = {Addison-Wesley},
  year = {2002},
  author = {A. Shalloway and J. R. Trott},
  address = {Boston, MA}
}

@ARTICLE{ShNW02,
  author = {M.~Shatsky and R.~Nussinov and H.~Wolfson},
  title = {Flexible Protein Alignment and Hinge Detection},
  journal = PROlong,
  year = {2002},
  volume = {48},
  pages = {242-256}
}

@ARTICLE{ShPa00,
  author = {Michael Shirts and Vijay S. Pande},
  title = {Screen Savers of the World Unite!},
  journal = {Science},
  year = {2000},
  volume = {290},
  pages = {1903-1904}
}

@ARTICLE{ShFr02,
  author = {Min-yi Shen and Karl F. Freed},
  title = {All-Atom Fast Protein Folding Simulations: The Villin Headpiece},
  journal = PRO,
  year = {2002},
  volume = {49},
  pages = {439-445}
}

@ARTICLE{ShFr02a,
  author = {Min-yi Shen and Karl F. Freed},
  title = {Long Time Dynamics of Met-Enkephalin: Comparison of Explicit and Implicit Solvent Models},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {82},
  pages = {1791-1808}
}

@ARTICLE{SkIz02,
  author = {R.~D. Skeel and J.~A. Izaguirre},
  title = {An Impulse Integrator for {L}angevin Dynamics},
  journal = MP,
  year = {2002},
  volume = {100},
  pages = {3885--3891},
  number = {24}
}

@ARTICLE{SkTH02,
  author = {R.~D. Skeel and I. Tezcan and D.~J. Hardy},
  title = {Multiple grid methods for classical molecular dynamics},
  journal = JCC,
  year = {2002},
  volume = {23},
  pages = {673--684},
  number = {6},
  annote = {Presented in the context of classical molecular mechanics and dynamics
	are multilevel summation methods for the fast calculation of energies/forces
	for pairwise interactions, which are based on the hierarchical interpolation
	of interaction potentials on multiple grids. The concepts and details
	underlying multigrid interpolation are described. For integration
	of molecular dynamics the use of different time steps for different
	interactions allows longer time steps for many of the interactions,
	and this can be combined with multiple grids in space. Comparison
	is made to the fast multipole method, and evidence is presented suggesting
	that for molecular simulations multigrid methods may be superior
	to the fast multipole method and other tree methods. http://www3.interscience.wiley.com/cgi-bin/issuetoc?ID=91016095}
}

@ARTICLE{SmDG02,
  author = {Lorna J. Smith and Xavier Daura and Wilfred F. van Gunsteren},
  title = {Assessing Equilibration and Convergence in Biomolecular Simulations},
  journal = PRO,
  year = {2002},
  volume = {48},
  pages = {487--496}
}

@ARTICLE{TKTT02,
  author = {H. Tosuji and T. Kishimoto and C. Totsuji and K. Tsuruta},
  title = {Competition between Two Forms of Ordering in Finite {C}oulomb Clusters},
  journal = PRL,
  year = {2002},
  volume = {88},
  number = {12}
}

@BOOK{Wolf02,
  title = {A new kind of science},
  publisher = {Wolfram Media, Inc.},
  year = {2002},
  author = {Stephen Wolfram},
  address = {Champaign, IL}
}

@PHDTHESIS{Zaja02,
  author = {M.~Zajac},
  title = {Modeling Convergent Extension by Way of Anisotopic Differential Adhesion},
  school = {University of Notre Dame, Notre Dame, Indiana, USA},
  year = {2002}
}

@CONFERENCE{ZLNG02,
  author = {W. Zeng and G. L. Thomas and S. A. Newman and J. A. Glazier},
  title = {A novel mechanism for mesenchymal condensation during limb chondrogenesis
	in vitro},
  booktitle = {Mathematical Modeling and Computing in Biology and Medicine: 5th
	Conference of the European Society of Mathematical and Theoretical
	Biology, Milan},
  year = {2002},
  pages = {80--86},
  publisher = {V. Capasso and M. Ortisi}
}

@INPROCEEDINGS{BaBr01,
  author = {D. Bai and A. Brandt},
  title = {Multiscale Algorithms in Molecular Dynamics},
  booktitle = {In Multiscale Computational Methods in Chemistry and Physics},
  year = {2001},
  editor = {A. Brandt and J. Bernholc and K. Binder},
  volume = {177},
  series = {{NATO} Science Series: Series {III} Computer and Systems Sciences},
  pages = {250--266},
  address = {Amsterdam, The Netherlands},
  month = APR,
  publisher = {IOS Press}
}

@INPROCEEDINGS{KMNI01,
  author = {Shannon Kuntz and Richard Murphy and Mike Niemier and J.~A. Izaguirre
	and Peter Kogge},
  title = {Petaflop Computing for Protein Folding},
  booktitle = {Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific
	Computing (PP01)},
  year = {2001},
  series = {Proceedings in Applied Mathematics},
  address = {Philadelphia},
  month = MAR,
  publisher = {Society for Industrial and Applied Mathematics},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/protopim.pdf}}
}

@BOOK{Leac01,
  title = {Molecular Modelling: Principles and Applications},
  publisher = {Prentice Hall},
  year = {2001},
  author = {Andrew R. Leach},
  edition = {2nd},
  month = MAR,
  nremark = {ISBN: 0582382106}
}

@INPROCEEDINGS{MaIz01,
  author = {T. Matthey and J.~A. Izaguirre},
  title = {Proto{M}ol: A Molecular Dynamics Framework with Incremental Parallelization},
  booktitle = {Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific
	Computing (PP01)},
  year = {2001},
  series = {Proceedings in Applied Mathematics},
  address = {Philadelphia},
  month = MAR,
  publisher = {Society for Industrial and Applied Mathematics},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/proto.pdf}}
}

@INBOOK{Izag01,
  pages = {34--47},
  title = {Generalized Mollified Multiple Time Stepping Methods for Molecular
	Dynamics},
  publisher = {IOS Press},
  year = {2001},
  editor = {A. Brandt and J. Bernholc and K. Binder},
  author = {J.~A. Izaguirre},
  volume = {177},
  series = {NATO Science Series: Series III Computer and Systems Sciences},
  address = {Amsterdam, The Netherlands},
  month = JAN,
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/eilat.pdf}},
  booktitle = {Multiscale Computational Methods in Chemistry and Physics}
}

@BOOK{Alex01,
  title = {Modern {C\texttt{++}} design: {G}eneric programming and design patterns
	applied},
  publisher = {Addison-Wesley},
  year = {2001},
  author = {A. Alexandrescu},
  address = {Reading, Massachusetts}
}

@ARTICLE{Ayt+01,
  author = {G. Ayton and S.G. Bardenhagen and P. McMurtry and D. Sulsky and G.A.
	Voth},
  title = {Interfacing continuum and molecular dynamics: An application to lipid
	bilayers},
  journal = JCP,
  year = {2001},
  volume = {114},
  number = {15}
}

@UNPUBLISHED{petsc-home-page,
  author = {Satish Balay and Kris Buschelman and William D. Gropp and Dinesh
	Kaushik and Lois Curfman McInnes and Barry F. Smith},
  title = {{PETSc} home page},
  note = {http://www.mcs.anl.gov/petsc},
  year = {2001}
}

@TECHREPORT{petsc-manual,
  author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry
	F. Smith},
  title = {{PETSc} Users Manual},
  institution = {Argonne National Laboratory},
  year = {2001},
  number = {ANL-95/11 - Revision 2.1.1}
}

@ARTICLE{BaCS01,
  author = {P.~F. Batcho and D.~A. Case and T. Schlick},
  title = {Optimized particle-mesh {E}wald/multiple-time step integration for
	molecular dynamics simulations},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {4003--4018},
  number = {9},
  annote = {We develop an efficient multiple time step ~MTS! force splitting
	scheme for biological applications in the AMBER program in the context
	of the particle-mesh Ewald ~PME! algorithm. Our method applies a
	symmetric Trotter factorization of the Liouville operator based on
	the position-Verlet scheme to Newtonian and Langevin dynamics. Following
	a brief review of the MTS and PME algorithms, we discuss performance
	speedup and the force balancing involved to maximize accuracy, maintain
	long-time stability, and accelerate computational times. Compared
	to prior MTS efforts in the context of the AMBER program, advances
	are possible by optimizing PME parameters for MTS applications and
	by using the position-Verlet, rather than velocity-Verlet, scheme
	for the inner loop. Moreover, ideas from the Langevin/MTS algorithm
	LN are applied to Newtonian formulations here. The algorithms performance
	is optimized and tested on water, solvated DNA, and solvated protein
	systems. We find CPU speedup ratios of over 3 for Newtonian formulations
	when compared to a 1 fssingle-step Verlet algorithm using outer time
	steps of 6 fs in a three-class splitting scheme; accurate conservation
	of energies is demonstrated over simulations of length several hundred
	ps. With modest Langevin forces, we obtain stable trajectories for
	outer time steps up to 12 fs and corresponding speedup ratios approaching
	5. We end by suggesting that modified Ewald formulations, using tailored
	alternatives to the Gaussian screening functions for the Coulombic
	terms, may allow larger time steps and thus further speedups for
	both Newtonian and Langevin protocols; such developments are reported
	separately.}
}

@ARTICLE{BaSc01,
  author = {P.~F. Batcho and T. Schlick},
  title = {Special stability advantages of position-Verlet over velocity-Verlet
	in multiple-time step integration},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {4019--4029},
  number = {9},
  annote = {We present an analysis for a simple two-component harmonic oscillator
	that compares the use of position-Verlet to velocity-Verlet for multiple-time
	step integration. The numerical stability analysis based on the impulse-Verlet
	splitting shows that position-Verlet has enhanced stability, in terms
	of the largest allowable time step, for cases where an ample separation
	of time scales exists. Numerical investigations confirm the advantages
	of the position-Verlet scheme when used for the fastest time scales
	of the system. Applications to a biomolecule, a solvated protein,
	for both Newtonian and Langevin dynamics echo these trends over large
	outer time-step regimes. (c) 2001 American Institute of Physics.}
}

@ARTICLE{BaSc01a,
  author = {P.~F. Batcho and T. Schlick},
  title = {New splitting formulations for lattice summations},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {8312--8326},
  number = {18},
  annote = {We present a new formulation for the efficient evaluation of pairwise
	interactions for large nonperiodic or spatially periodic infinite
	lattices. Our optimally designed splitting formulation generalizes
	the Ewald method and its Gaussian core function. In particular, we
	show that a polynomial multiplication to the Gaussian core function
	can be used to formulate desired mathematical or physical characteristics
	into a lattice summation method. Two optimization statements are
	examined. The first incorporates a pairwise interaction splitting
	into the lattice sum, where the direct (real) and reciprocal space
	terms also isolate the near-field and far-field pairwise particle
	interactions, respectively. The second optimization defines a splitting
	with a rapidly convergent reciprocal space term that allows enhanced
	decay rates in the real-space term relative to the traditional Ewald
	method. These approaches require modest adaptation to the Ewald formulation
	and are expected to enhance performance of particle-mesh methods
	for large-scale systems. A motivation for future applications is
	large-scale biomolecular dynamics simulations using particle-mesh
	Ewald methods and multiple time step integration. (c) 2001 American
	Institute of Physics.}
}

@ARTICLE{BAUD2001,
  author = {Jerome Baudry and Emad Tajkhorshid and Ferenc Molnar and James Phillips
	and Klaus Schulten},
  title = {Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane},
  journal = JPCB,
  year = {2001},
  volume = {105(5)},
  pages = {905--918},
  note = {Invited feature article.}
}

@INPROCEEDINGS{BHAN01,
  author = {M. Bhandarkar and R. Brunner and A. Dalke and J. Gullingsrud and
	A. Gursoy and W. Humphrey and D. Hurwitz and N. Krawetz and M. Nelson
	and J. Phillips and A. Shinozaki and G. Zheng and F. Zhu},
  title = {NAMD User's Guide: Version 2.3b2},
  year = {2001},
  pages = {11},
  address = {405 N. Mathews, Urbana, IL 61801},
  publisher = {Theoretical Biophysics Group at the University of Illinos and Beckman
	Institute}
}

@CONFERENCE{ChKe01,
  author = {A. Chauhan and K. Kennedy},
  title = {Optimizing Strategies for Telescoping Languages: Procedure Strength
	Reduction and Procedure Vectorization},
  booktitle = {Proceedings of Supercomputing~'01},
  year = {2001},
  pages = {92--101},
  organization = {ACM/IEEE Computer Society}
}

@ARTICLE{CBRL01,
  author = {H. Clauben and C. Buning and M. Rarey and T. Lengauer},
  title = {Flex{E}: {E}fficient molecular docking considering protein structure
	variations},
  journal = JMB,
  year = {2001},
  volume = {308},
  pages = {377--395}
}

@ARTICLE{CoCP01,
  author = {D. M. Cortes and L. G. Cuello and E. Perozo},
  title = {Molecular Architecture of Full-Length {K}cs{A}},
  journal = {J. Gen Physiology},
  year = {2001},
  volume = {117},
  pages = {165--180}
}

@ARTICLE{CRAI2001,
  author = {David Craig and Andr{\'e} Krammer and Klaus Schulten and Viola Vogel},
  title = {Comparison of the early stages of forced unfolding of fibronectin
	type III modules},
  journal = PNAS,
  year = {2001},
  note = {Submitted.}
}

@INCOLLECTION{Dill01,
  author = {Robert Dillon},
  title = {Mathematical modeling of vertebrate limb development},
  booktitle = {Pattern Formation and Morphogenesis: Model systems},
  publisher = {IMA},
  year = {2001},
  volume = {121},
  series = {IMA Volumes in Mathematics and its Applications},
  pages = {39--57}
}

@MISC{Duan01,
  author = {Y. Duan},
  title = {Dept. of Chemistry, {U}. of {D}elaware},
  howpublished = {personal communication},
  year = {2001}
}

@ARTICLE{DuKo01,
  author = {Y. Duan and P. A. Kollman },
  title = {Computational protein folding: From lattice to all-atom},
  journal = {Deep computing for the life sciences},
  year = {2001},
  volume = {40},
  number = {2}
}

@ARTICLE{DuKr01,
  author = {Z. H. Duan and R. Krasny},
  title = {An Adaptive Treecode for Computing Nonbonded Potential Energy in
	Classical Molecular Systems},
  journal = JCC,
  year = {2001},
  volume = {22},
  pages = {184--195},
  number = {2}
}

@ARTICLE{ESAG01,
  author = {R. Edwards and H. T. Siegelmann and K. Aziza and L. Glass},
  title = {Symbolic dynamics and computation in model gene networks},
  journal = {Chaos},
  year = {2001},
  volume = {11},
  pages = {160--169},
  number = {1}
}

@ARTICLE{FORS2001,
  author = {Christian Forst and Klaus Schulten},
  title = {Phylogenetic Analysis of Metabolic Pathways},
  journal = {Journal of Molecular Evolution},
  year = {2001},
  note = {In Press.}
}

@ARTICLE{GiMi01,
  author = {J. Giavitto and O. Michel},
  title = {{MGS}: a Rule-Based Programming Language for Complex Objects and
	Collections},
  journal = {Electronic Notes in Theoretical Computer Science},
  year = {2001},
  volume = {59},
  number = {4}
}

@ARTICLE{GULL2001,
  author = {Justin Gullingsrud and Dorina Kosztin and Klaus Schulten},
  title = {Structural Determinants of {M}scl Gating Studied by Molecular Dynamics
	Simulations},
  journal = BJ,
  year = {2001},
  note = {In Press.}
}

@MISC{HARD01,
  author = {David J. Hardy},
  title = {Theoretical Biophysics Group, University of Illinois at Urbana-Champaign},
  howpublished = {http://www.ks.uiuc.edu/Development/MDTools/mdapi},
  year = {2001}
}

@INPROCEEDINGS{ISRA2001A,
  author = {B. Isralewitz and J. Baudry and J. Gullingsrud and D. Kosztin and
	K. Schulten},
  title = {Steered Molecular Dynamics Investigations of Protein Function},
  booktitle = {Journal of Molecular Graphics and Modeling},
  year = {2001},
  editor = {L. A. Kuhn and M. F. Thorpe},
  volume = {19},
  note = {also in {\it Protein Flexibility and Folding}}
}

@ARTICLE{ISRA2001,
  author = {B. Isralewitz and M. Gao and K. Schulten},
  title = {Steered Molecular Dynamics and Mechanical Functions of Proteins},
  journal = COSB,
  year = {2001},
  volume = {11},
  pages = {224--230}
}

@ARTICLE{ICWS01,
  author = {J.~A. Izaguirre and D.~P. Catarello and J.~M. Wozniak and R.~D. Skeel},
  title = {Langevin Stabilization of Molecular Dynamics},
  journal = JCP,
  year = {2001},
  volume = {114},
  pages = {2090--2098},
  number = {5}
}

@UNPUBLISHED{IMW+01,
  author = {J.~A. Izaguirre and T. Matthey and J. Willcock and Q. Ma and B. Moore
	and T. Slabach and G. Viamontes},
  title = {A Tutorial on the Prototyping of Multiple Time Stepping Integrators
	for Molecular Dynamics},
  note = {Available from \texttt{\small http://www.cse.nd.edu/\~{}lcls/Protomol.html}},
  year = {2001}
}

@ARTICLE{KaMi01,
  author = {M. Kawata and M. Mikami},
  title = {Rapid calculation of two-dimensional {E}wald summation},
  journal = {Chemical Physics Letters},
  year = {2001},
  volume = {340},
  pages = {157--164},
  number = {1-2},
  annote = {A computationally efficient method was developed to implement the
	Ewald summation in calculations for Coulomb interactions in three-dimensional
	(3D) systems with two-dimensional (2D) periodicity. The computational
	efficiency and accuracy of this method was evaluated for water systems
	enclosed in various rectangular parallelepiped boxes (cube, quadratic
	prism, and slab) and with 2D periodicity. Compared with existing
	computational methods, this method showed a significant reduction
	in computational time for all systems examined and was sufficiently
	accurate for calculating the Coulomb interactions in 3D systems with
	2D periodicity, independent of the shape of the simulation box.}
}

@ARTICLE{KaNa01,
  author = {M. Kawata and U. Nagashima},
  title = {Particle mesh {E}wald method for three-dimensional systems with two-dimensional
	periodicity},
  journal = {Chemical Physics Letters},
  year = {2001},
  volume = {340},
  pages = {165--172},
  number = {1-2},
  annote = {A particle mesh Ewald method for calculating Coulomb interactions
	in three-dimensional (3D) systems with two-dimensional (2D) periodicity
	was developed. Computational efficiency and accuracy of this method
	were evaluated for a TIP3P water system with 2928 particles in a
	cubic box with 2D periodicity. The accuracy of this method for calculating
	Coulomb interactions is comparable to our previous method that uses
	Fourier integral. For calculations with maximum errors in the Coulomb
	force of 0.4-20.0 kJmol-1 nm-1, the current method was up to five
	times faster than the previous method.}
}

@ARTICLE{LaHC01,
  author = {D.~J. Langridge and J. F. Hart and S. Crampin},
  title = {Ewald summation technique for one-dimensional charge distributions},
  journal = CPC,
  year = {2001},
  volume = {134},
  pages = {78--85},
  number = {1},
  annote = {We address the numerical evaluation of problematic lattice sums that
	occur when dealing with long-range electrostatic interactions in
	systems with one-dimensional periodicity. An Ewald-type solution
	is developed yielding rapidly convergent sums. Explicit expressions
	are given for the Madelung matrices that enter the potential and
	total energy in self-consistent electronic structure calculations
	for systems such as atomic wires and steps.}
}

@ARTICLE{LaMu01,
  author = {H.~P.~Langtangen and O.~Munthe},
  title = {Solving Systems of Partial Differential Equations Using Object-Oriented
	Programming Techniques with Coupled Heat and Fluid Flow as Examples},
  journal = ACMTMS,
  year = {2001},
  volume = {27},
  pages = {1--26},
  number = {1},
  annote = {http://www.ifi.uio.no/~hpl/}
}

@ARTICLE{LeRe01,
  author = {B. Leimkuhler and S. Reich},
  title = {A reversible averaging integrator for multiple time-scale dynamics},
  journal = {J. Comput. Phys.},
  year = {2001},
  volume = {171},
  pages = {95--114}
}

@ARTICLE{LiHS01,
  author = {E. Lindahl and B. Hess and D. van der Spoel},
  title = {{GROMACS 3.0}: A package for molecular simulation and trajectory},
  journal = JMM,
  year = {2001},
  volume = {7},
  pages = {306--317},
  number = {8}
}

@ARTICLE{MaHo01,
  author = {A. F. M. Mar{\'e}e and P. Hogeweg},
  title = {How amoeboids self-organize into a fruiting body: {M}ulticellular
	coordination in \emph{{D}ictyostelium discoideum}},
  journal = PNAS,
  year = {2001},
  volume = {98},
  pages = {3879--3883},
  number = {7}
}

@CONFERENCE{MiVa01,
  author = {L. Michel and P. Van~Hentenryck},
  title = {Modeler++, A Modeling Layer for Constraint Programming Libraries},
  booktitle = {Proceedings of CP-AI-OR'2001},
  year = {2001},
  publisher = {Wye College (Imperial College), Ashford, Kent UK}
}

@ARTICLE{MAT+01,
  author = {J.~C. M. Mombach and R.~M. C. de Almeida and G.~L. Thomas and A.~Upadhyaya
	and J.~A. Glazier},
  title = {Bursts and cavity formation in {\it Hydra} cell aggregates: experiments
	and simulations},
  journal = {Physica A},
  year = {2001},
  volume = {297},
  pages = {495--508},
  number = {3--4}
}

@ARTICLE{PMMS01,
  author = {K. M. Page and P. K. Maini and N. A. M. Monk and C. D. Stern},
  title = {A model of primitive streak initiation in the chick embryo},
  journal = JTB,
  year = {2001},
  volume = {208},
  pages = {419--438}
}

@ARTICLE{PaFr01,
  author = {I Pagonabarraga and D Frenkel},
  title = {Dissipative Particle Dynamics for Interacting Systems},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {5015--5026},
  number = {11}
}

@MISC{PMV01,
  author = {PMV},
  title = {Python Molecular Viewer},
  howpublished = {\url{http://www.scripps.edu/~sanner/python/pmv/webpmv.html}},
  year = {2001},
  annote = {PMV Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{PrSB01,
  author = {J. J. Prompers and C. Scheurer and R. Br{\"u}schweiler},
  title = {Characterization of {NMR} Relaxation-Active Motions of a Partially
	Folded {A}-State Analogue of Ubiquitin},
  journal = {J. Mol. Biol.},
  year = {2001},
  volume = {305},
  pages = {1085--1097}
}

@ARTICLE{RITZ2001A,
  author = {Thorsten Ritz and Ana Damjanovi\'{c} and Klaus Schulten and {Jian-Ping}
	Zhang and Yasushi Koyama},
  title = {Efficient Light Harvesting Through Carotenoids},
  journal = {Photosynthesis Research},
  year = {2001},
  note = {In press.}
}

@ARTICLE{RITZ2001,
  author = {Thorsten Ritz and Klaus Schulten},
  title = {Physik der {P}hotosynthese},
  journal = {Physikalische Blaetter},
  year = {2001},
  volume = {57(2)},
  pages = {49--53}
}

@ARTICLE{SaDa01,
  author = {C. Sagui and T. Darden},
  title = {Multigrid methods for classical molecular dynamics simulations of
	biomolecules},
  journal = JCP,
  year = {2001},
  volume = {114},
  pages = {6578--6591},
  number = {15},
  annote = {We present an O(N) multigrid-based method for the efficient calculation
	of the long-range electrostatic forces needed for biomolecular simulations,
	that is suitable for implementation on massively parallel architectures.
	Along general lines, the method consists of: (i) a charge assignment
	scheme, which both interpolates and smoothly assigns the charges
	onto a grid; (ii) the solution of Poisson's equation on the grid
	via multigrid methods; and (iii) the back interpolation of the forces
	and energy from the grid to the particle space. Careful approaches
	for the charge assignment and the force interpolation, and a Hermitian
	approximation of Poisson's equation on the grid allow for the generation
	of the high-accuracy solutions required for high-quality molecular
	dynamics simulations. Parallel versions of the method scale linearly
	with the number of particles for a fixed number of processors, and
	with the number of processors, for a fixed number of particles.}
}

@ARTICLE{Sand01,
  author = {B. Sandak},
  title = {Multiscale Fast Summation of Long-Range Charge and Dipolar Interactions},
  journal = JCC,
  year = {2001},
  volume = {22},
  pages = {717--731},
  number = {7},
  abstract = {Here we present a linear order multiscale method for the fast summation
	of long range forces in a system consisting of a large number of
	charge and dipolar particles. For a N-body system, our algorithm
	requires an order of work that is proportional to O(N), in comparison
	to order O(N-2) of the direct pairwise computation. Our method is
	demonstrated on two-dimensional homogeneous point-charge and dipolar
	systems, and a combined heterogeneous particle system, for the calculation
	of the induced electrostatic potential and energy. The electrostatic
	interaction is decomposed into a local part and a smooth part. The
	method thus, has several potential advantages over other O(N log
	N) or O(N) techniques, especially for calculation with moving particles
	or implicit charges locations. This approach is beneficial to large-scale
	problems such as molecular statics, molecular dynamics, equilibrium
	statistics ({M}onte {C}arlo simulations), molecular docking, and
	in areas such as magnetism and astrophysics.}
}

@ARTICLE{Schl01,
  author = {T.~Schlick},
  title = {Time-trimming tricks for dynamics simulations:Splitting force updates
	to reduce computational work},
  journal = STR,
  year = {2001},
  volume = {9},
  pages = {R45-R53}
}

@ARTICLE{ShPa01,
  author = {Michael R. Shirts and Vijay S. Pande},
  title = {Mathematical Analysis of Coupled Parallel Simulations},
  journal = PRL,
  year = {2001},
  volume = {86},
  pages = {4983--4987},
  number = {22}
}

@ARTICLE{SkHa01,
  author = {R.~D. Skeel and D.~J. Hardy},
  title = {Practical construction of modified {H}amiltonians},
  journal = SJSC,
  year = {2001},
  volume = {23},
  pages = {1172--1188},
  number = {4}
}

@ARTICLE{SPIN01,
  author = {D. Spinellis},
  title = {Notable Design Patterns For Domain-Specific Languages},
  journal = {Journal of Systems and Software},
  year = {2001},
  volume = {56},
  pages = {91--99}
}

@INPROCEEDINGS{STON2000,
  author = {J. Stone and J. Gullingsrud and K. Schulten},
  title = {A System for Interactive Molecular Dynamics},
  booktitle = {2001 Symposium on Interactive 3D Graphics},
  year = {2001},
  publisher = {ACM},
  note = {In Press.},
  annote = {This symposium will take place between March 19-21, 2001}
}

@ARTICLE{SuSR01,
  author = {Marius Sudol and Krzysztof Sliwa and Tommaso Russo},
  title = {Functions of WW domains in the nucleus},
  journal = {FEBS Letters},
  year = {2001},
  volume = {490},
  pages = {190--195}
}

@ARTICLE{SuHu00,
  author = {M. Sudol and T. Hunter},
  title = {New wrinkles of an old domain},
  journal = {Cell},
  year = {2000},
  volume = {103},
  pages = {1001--1004}
}

@ARTICLE{TamS01,
  author = {F.~Tama and Y.~H.~Sanejouand},
  title = {Conformational changes of proteins arising from normal mode calculations},
  journal = PE,
  year = {2001},
  volume = {14},
  pages = {1-6},
  number = {1}
}

@BOOK{TrCh01,
  title = {Data Structures and Software Development in an Object-Oriented Domain},
  publisher = {Prentice Hall},
  year = {2001},
  author = {Jean Paul Tremblay and Grant A. Cheston},
  address = {Upper Saddle River, NJ}
}

@ARTICLE{UVD+01,
  author = {J. C. Uitdehaag and B. A. Van der Veen and L. Dijkhuizen and R. Elber
	and B. W. Dijkstra},
  title = {Enzymatic Circularization of a Malto-Octaose Linear Chain Studied
	by Stochastic Reaction Path Calculations on Cyclodextrin Glycosyltransferase.},
  journal = {Proteins},
  year = {2001},
  volume = {43},
  pages = {327--335},
  number = {3}
}

@ARTICLE{UVDE+01,
  author = {J. C. Uitdehaag and B. A. Van der Veen and L. Dijkhuizen and R. Elber
	and B. W. Dijkstra},
  title = {Enzymatic Circularization of a Malto-Octaose Linear Chain Studied
	by Stochastic Reaction Path Calculations on Cyclodextrin Glycosyltransferase.},
  journal = {Proteins},
  year = {2001},
  volume = {43},
  pages = {327--335},
  number = {3}
}

@ARTICLE{URG+01,
  author = {A.~Upadhyaya and J.~P. Rieu and J.~A. Glazier and Y.~Sawada},
  title = {Anomalous diffusion in two-dimensional {\em Hydra} cell aggregates},
  journal = {Physica A},
  year = {2001},
  volume = {293},
  pages = {549--558},
  number = {3--4}
}

@ARTICLE{WaHo01,
  author = {Z. Wang and C. Holm},
  title = {Estimate of the cutoff errors in the {E}wald summation for dipolar
	systems},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {6351--6359},
  number = {14},
  annote = {Theoretical estimates for the cutoff errors in the Ewald summation
	method for dipolar systems are derived. Absolute errors in the total
	energy, forces and torques, both for the real and reciprocal space
	parts, are considered. The applicability of the estimates is tested
	and confirmed in several numerical examples. We demonstrate that
	these estimates can be used easily in determining the optimal parameters
	of the dipolar Ewald summation in the sense that they minimize the
	computation time for a predefined, user set, accuracy.}
}

@ARTICLE{WWDR01,
  author = {R. Wintjens and J.M. Wieruszeski and H. Drobecq and P. Rousselot-Pailley
	and L. Buee and G. Lippens and I. Landrieu},
  title = {1H {NMR} study on the binding of {PIN1} Trp-Trp domain with phosphothreonine
	peptides},
  journal = JBC,
  year = {2001},
  volume = {276},
  pages = {25150--25156}
}

@ARTICLE{YGSR01,
  author = {D. Y. Yang and A. Grama and V. Sarin and K. Ramakrishnan},
  title = {Compression of Particle Data from Hierarchical Approximate Methods},
  journal = ACMTMS,
  year = {2001},
  volume = {27},
  pages = {317--339},
  number = {3}
}

@ARTICLE{YuKo01,
  author = {M. R. Yudt and S. Koide},
  title = {Preventing estrogen receptor action with dimer-interface peptides},
  journal = {Steroids},
  year = {2001},
  volume = {66},
  pages = {549--558}
}

@ARTICLE{ZhBG01,
  author = {Ruhong Zhou and Bruce J. Berne and Robert Germain},
  title = {The free energy landscape for $\Beta$ hairpin folding in explicit
	water},
  journal = PNAS,
  year = {2001},
  volume = {98},
  pages = {14931--14936}
}

@ARTICLE{ZHXB01,
  author = {R. Zhou and E. Harder and H. Xu and B.~J. Berne},
  title = {Efficient multiple time step method for use with {E}wald and particle
	mesh {E}wald for large biomolecular systems},
  journal = JCP,
  year = {2001},
  volume = {115},
  pages = {2348--2358},
  number = {5},
  annote = {The particle-particle-particle-mesh (P3M) method for calculating
	long-range electrostatic forces in molecular simulations is modified
	and combined with the reversible reference system propagator algorithm
	~RESPA! for treating the multiple time scale problems in the molecular
	dynamics of complex systems with multiple time scales and long-range
	forces. The resulting particle-particle particle-mesh Ewald RESPA
	~P3ME/RESPA! method provides a fast and accurate representation of
	the long-range electrostatic interactions for biomolecular systems
	such as protein solutions. The method presented here uses a different
	breakup of the electrostatic forces than was used by other authors
	when they combined the Particle Mesh Ewald method with RESPA. The
	usual breakup is inefficient because it treats the reciprocal space
	forces in an outer loop even though they contain a part that changes
	rapidly in time. This does not allow use of a large time step for
	the outer loop. Here, we capture the short-range contributions in
	the reciprocal space forces and include them in the inner loop, thereby
	allowing for larger outer loop time steps and thus for a much more
	efficient RESPA implementation. The new approach has been applied
	to both regular Ewald and P3ME. The timings of Ewald/RESPA and P3ME/RESPA
	are compared in detail with the previous approach for protein water
	solutions as a function of number of atoms in the system, and significant
	speedups are reported.}
}

@MISC{BOB0x,
  author = {Department of Chemistry and Biochemistry},
  title = {{B}o{B}: Bunch-o-Boxes Beowulf cluster},
  howpublished = {Available online via {\small \texttt{http://bob.nd.edu/}}},
  year = {2000--2003},
  annote = {From Dr. Maginn: The computers were purchased with funds from the
	National Science Foundation under grant DMR-0079647. Please cite
	this, and when and papers are published or you graduate, please send
	an email to Olaf Wiest (owiest) so that he can include this information
	in the annual report to NSF. They love to hear how good their investment
	has been...}
}

@PHDTHESIS{Horn00,
  author = {L. Hornek{\ae}r},
  title = {Single- and Multi-Species Coulomb Ion Crystals: Structures, Dynamics
	and Sympathetic Cooling},
  school = {University of Aarhus},
  year = {2000},
  address = {Denmark},
  month = NOV
}

@PHDTHESIS{Mare00,
  author = {A. F. M. Mar\'ee},
  title = {From Pattern Formation to Morphogenesis},
  school = {Utrecht University},
  year = {2000},
  address = {Netherlands},
  month = OCT
}

@INCOLLECTION{MaHa00,
  author = {T. Matthey and J. P. Hansen},
  title = {Evaluation of {MPI}'s One-Sided Communication Mechanism for Short-Range
	Molecular Dynamics on the {O}rigin2000},
  booktitle = {Applied Parallel Computing. New Paradigms for {HPC} in Industry and
	Academia},
  publisher = {Springer-Verlag},
  year = {2000},
  editor = {T. S{\o}revik and F. Manne and R. Moe and A.~H. Gebremedhin},
  volume = {1947},
  series = {In Lecture Notes in Computer Science},
  pages = {374--365},
  address = {Bergen, Norway},
  month = JUN
}

@INPROCEEDINGS{Izag00,
  author = {J.~A. Izaguirre},
  title = {Generalized Mollified Multiple Time Stepping Methods for Molecular
	Dynamics},
  booktitle = {Multiscale Computational Methods in Chemistry and Biology},
  year = {2000},
  editor = {A. Brandt and K. Binder and J. Bernholc},
  address = {Amsterdam, Netherlands},
  month = APR,
  publisher = {IOS Press},
  note = {to appear}
}

@INPROCEEDINGS{Skee00,
  author = {R.~D. Skeel},
  title = {Multilevel Summation Methods for {N}-body Interactions},
  booktitle = {Multiscale Computational Methods in Chemistry and Biology},
  year = {2000},
  editor = {A. Brandt and K. Binder and J. Bernholc},
  address = {Amsterdam, Netherlands},
  month = APR,
  publisher = {IOS Press},
  note = {to appear}
}

@TECHREPORT{WhPD00,
  author = {R. Clint Whaley and Antoine Petitet and Jack J. Dongarra},
  title = {Automated Empirical Optimizations of Software and the ATLAS project},
  institution = {University of Tennessee, Knoxville, TN},
  year = {2000},
  address = {Department of Computer Science, Univ. of TN, Knoxville, TN 37996},
  month = APR,
  annote = {AEOS paper describing automated optimizations.}
}

@ARTICLE{AJOU2000,
  author = {Bassam Ajouz and Catherine Berrier and Madeleine Besnard and Boris
	Martinac and Alexandre Ghazi},
  title = {Contributions of the different extramembranous domains of the mechanosensitive
	ion channel \mbox{MscL} to its response to membrane tension},
  journal = JBC,
  year = {2000},
  volume = {275},
  pages = {1015--1022},
  number = {2}
}

@ARTICLE{AlLC00,
  author = {M. S. Alber and G. G. Luther and C. Miller},
  title = {On Soliton-type Solutions of the Equations Associated with N-component
	Systems},
  journal = {J. Math. Phys.},
  year = {2000},
  volume = {41},
  pages = {284--316}
}

@ARTICLE{AUBE2000,
  author = {C. Aubert and M.H. Vos and P. Mathis and A.P.M. Eker and K. Bretter},
  title = {Intraprotein radical transfer during photoactivation of {DNA} photolyase},
  journal = NAT,
  year = {2000},
  volume = {405},
  pages = {586--590}
}

@ARTICLE{Bake00,
  author = {D. Baker},
  title = {A Surprising Simplicity to Protein Folding},
  journal = NAT,
  year = {2000},
  volume = {405},
  pages = {39--42}
}

@ARTICLE{BaHW00,
  author = {N.~Baker and M.~Holst and E.~Wang},
  title = {Adaptive multilevel finite element solution of the Poisson-Boltzmann
	equation II. Refinement at solvent accessible surfaces in biomolecular
	systems},
  journal = JCC,
  year = {2000},
  volume = {21},
  pages = {1343-1352}
}

@ARTICLE{Bass00,
  author = {J.~B. Bassingthwaighte},
  title = {Strategies for the {P}{H}{Y}{S}{I}{O}{M}{E} project},
  journal = {Ann. Biomed. Eng.},
  year = {2000},
  volume = {28},
  pages = {1043--1058},
  number = {8}
}

@ARTICLE{BeSc00a,
  author = {Daniel A. Beard and Tamar Schlick},
  title = {Inertial stochastic dynamics. 1. Long-time-tep methods for Langevin
	dynamics},
  journal = {J. Chem. Phys.},
  year = {2000},
  volume = {112},
  pages = {7313--7322},
  number = {17}
}

@ARTICLE{BeSc00b,
  author = {Daniel A. Beard and Tamar Schlick},
  title = {Inertial stochastic dynamics. 11. Influence of inertia on slow kinetic
	processes of supercoiled DNA},
  journal = {J. Chem. Phys.},
  year = {2000},
  volume = {112},
  pages = {7323--7338},
  number = {17}
}

@ARTICLE{Berm00,
  author = {H. M. Berman and J. Westbrook and Z. Feng and G. Gilliland and T.
	N. Bhat and H. Weissig and I. N. Shindyalov and P. E. Bourne},
  title = {The Protein Data Bank},
  journal = {Nucleic Acids Research},
  year = {2000},
  pages = {235--242},
  readme = {See http://www.rcsb.org/pdb/citing.html for citing instructions.},
  url = {http://www.pdb.org/}
}

@ARTICLE{BERN2000,
  author = {Simon Bern{\`e}che and Benoit Roux},
  title = {Molecular Dynamics of the {KcsA} {K$^+$} channel in a bilayer membrane},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {2900--2917},
  number = {6}
}

@ARTICLE{BVKP00,
  author = {Gerhard Besold and Ilpo Vattulainen and Mikko Kartunnen and James
	M. Polson},
  title = {Towards Better Integrators for Dissipative Particle Dynamics Simulations},
  journal = {Physical Review E},
  year = {2000},
  volume = {62},
  pages = {R7611--R7614},
  number = {6}
}

@ARTICLE{BeFG00,
  author = {D. A. Beysens and G. Forgacs and J. A. Glazier},
  title = {Cell sorting is analogous to phase ordering in fluids},
  journal = PNAS,
  year = {2000},
  volume = {97},
  pages = {9467--9471}
}

@ARTICLE{BeFG00a,
  author = {D. A. Beysens and G. Forgacs and J. A. Glazier},
  title = {Embryonic tissues are viscoelastic materials},
  journal = {Canadian Journal of Physics},
  year = {2000},
  volume = {78},
  pages = {243--251},
  number = {3}
}

@ARTICLE{BeFG00b,
  author = {D. A. Beysens and G. Forgacs and J. A. Glazier},
  title = {Cell sorting is analogous to phase ordering in fluids},
  journal = PNAS,
  year = {2000},
  volume = {97},
  pages = {9467--9471},
  number = {17}
}

@ARTICLE{BOAR2000,
  author = {John Board and Klaus Schulten},
  title = {The Fast Multipole Algorithm},
  journal = IEEECSE,
  year = {2000},
  volume = {2},
  pages = {56--59}
}

@ARTICLE{BoFR00,
  author = {D. Bonachea and K. Fisher and A. Rogers},
  title = {Hancock: A language for processing very large-scale data},
  journal = {\it ACM Sigplan Notices},
  year = {2000},
  volume = {35},
  pages = {163--176},
  number = {1}
}

@PHDTHESIS{Bond00,
  author = {Stephen~D. Bond},
  title = {Numerical Methods for Extended {H}amiltonian Systems with Applications
	in Statistical Mechanics},
  school = {University of Kansas},
  year = {2000},
  address = {Lawrence, Kansas}
}

@ARTICLE{Brou00,
  author = {Howard B. Broughton},
  title = {A method for including protein flexibility in protein-ligand docking:
	{I}mproving tools for database mining and virtual screening},
  journal = JMGM,
  year = {2000},
  volume = {18},
  pages = {247--257},
  number = {3},
  www = {http://www.sciencedirect.com/science/article/B6TGP-416C1K7-4/2/3b41833650f2d728354d0d9d921ff86d}
}

@ARTICLE{BrFJ00,
  author = {P. N. Brown and R. D. Falgout and J. E. Jones},
  title = {Semicoarsening Multigrid on Distributed Memory Machines},
  journal = SJSC,
  year = {2000},
  volume = {21},
  pages = {1823--1834},
  number = {5},
  nremark = {Iterative multigrid parallel model and experimental results}
}

@ARTICLE{BuJa00,
  author = {A. Buchstaller and D. G. Jay},
  title = {Micro-scale chromophore-assisted laser inactivation of nerve growth
	cone proteins},
  journal = {Microscopy Research and Technique},
  year = {2000},
  volume = {48},
  pages = {97--106},
  number = {2}
}

@BOOK{BuMa00,
  title = {Efficient {C\texttt{++}} - Performance programming techniques},
  publisher = {Addison-Wesley},
  year = {2000},
  author = {D. Bulka and D. Mayhew}
}

@ARTICLE{CMRB00,
  author = {Heather A. Carlson and Kevin M. Masukawa and Kathleen Rubins and
	Fredric D. Bushman and William L. Jorgensen and Roberto D. Lins and
	James M. Briggs and J. Andrew McCammon},
  title = {Developing a Dynamic Pharmacophore Model for HIV-1 Integrase},
  journal = JMC,
  year = {2000},
  volume = {43},
  pages = {2100--2114}
}

@ARTICLE{CaMc00,
  author = {Heather A. Carlson and J. Andrew McCammon},
  title = {Accomodating Protein Flexibility in Computational Drug Design},
  journal = {Molecular Pharmacology},
  year = {2000},
  volume = {57},
  pages = {213--218}
}

@ARTICLE{CPCW00,
  author = {H. M. Chun and C. E. Padilla and D. N. Chin and M. Waranabe and V.
	I. Karlov and H. E. Alper and K. Soosaar and K. B. Blair and O. M.
	Becker and L. S. D. Caves and R. Nagle and D. N. Haney and B. L.
	Farmer},
  title = {MBO(N)D: {A} Multibody Method for Long-Time Molecular Dynamics Simulations},
  journal = {J. of Comp. Chem.},
  year = {2000},
  volume = {21},
  pages = {159--184}
}

@ARTICLE{ClPi00,
  author = {D.~E. Clark and S.~D. Pickett},
  title = {Computational methods for the prediction of 'drug-likeness'},
  journal = {Drug Discovery Today},
  year = {2000},
  volume = {5},
  number = {2},
  note = {Elsevier Science Ltd.}
}

@ARTICLE{CrCh00,
  author = {Gavin E. Crooks and David Chandler},
  title = {Efficient Transition Path Sampling for Nonequilibrium Stochastic
	Dynamics},
  journal = pre,
  year = {2000},
  volume = {64},
  pages = {26109},
  abstract = {The transition path sampling methodology is adapted to the efficient
	sampling of large fluctuations in nonequilibrium systems evolving
	according to Langevins equations of motion. This technique is used
	to simulate the behavior of the bistable Maier-Stein system at noise
	intensities much lower than those previously possible.}
}

@BOOK{CzEi00,
  title = {Generative Programming - Methods, Tools, and Application},
  publisher = {Addison Wesley},
  year = {2000},
  author = {K. Czarnecki and U.~W. Eisenecker}
}

@ARTICLE{DAMJ2000,
  author = {Ana Damjanovi\'c and Thorsten Ritz and Klaus Schulten},
  title = {Excitation Energy Trapping by the Reaction Center of {{\em Rhodobacter
	sphaeroides}}},
  journal = {Int.\ J.\ Quantum Chem.},
  year = {2000},
  note = {In press.}
}

@ARTICLE{DAMJ2000A,
  author = {Ana Damjanovi\'c and Thorsten Ritz and Klaus Schulten},
  title = {Excitation Transfer in the Peridinin-Chlorophyll-Protein of {{\it
	Amphidinium carterae}}},
  journal = BJ,
  year = {2000},
  volume = {79},
  pages = {1695--1705}
}

@MISC{Dare00,
  author = {Frederica Darema},
  title = {Senior Science and Technology Advisor, CISE, NSF},
  howpublished = {personal communication},
  year = {2000}
}

@ARTICLE{VaKV00,
  author = {A. van Deursen and P. Klint and J. Visser},
  title = {Domain-Specific Languages: An Annotated Bibliography},
  journal = {ACM SIGPLAN Notices},
  year = {2000},
  volume = {35},
  pages = {26--36},
  number = {6}
}

@ARTICLE{DrFo00,
  author = {Dirk Drasdo and Gabor Forgacs},
  title = {Interplay of Generic and Genetic Mechanisms in Early Development},
  journal = {Developmental Dynamics},
  year = {2000},
  volume = {219},
  pages = {182--191}
}

@ARTICLE{DuKr00,
  author = {Z. H. Duan and R. Krasny},
  title = {An {E}wald summation based multipole method},
  journal = JCP,
  year = {2000},
  volume = {113},
  pages = {3492--3495},
  number = {9},
  annote = {We present a method for evaluating Coulomb interactions in periodic
	molecular systems. The real space term in Ewald summation is accelerated
	using a tree code in which interactions between clusters and distant
	particles are approximated by multipole expansions. The performance
	is reported for water systems.}
}

@BOOK{ElNa00,
  title = {Fundamentals of Database Systems: 3rd Edition},
  publisher = {Addison-Wesley},
  year = {2000},
  author = {R. Elmasri and S. B. Navathe}
}

@INPROCEEDINGS{EGGL00,
  author = {R. Esser and P. Grassberger and J. Grotendorst and M. Lewerenz},
  title = {{EGO} -- An efficient molecular dynamics program and its application
	to protein dynamics simulations},
  booktitle = {Workshop on Molecular Dynamics on Parallel Computers},
  year = {2000},
  series = {World Scientific},
  pages = {154--174},
  address = {Singapore 912805}
}

@BOOK{Fish00,
  title = {{M}onte {C}arlo: Concepts, Algorithms, and Applications},
  publisher = {Springer-Verlag},
  year = {2000},
  author = {George S. Fishman},
  series = {Springer Series in Operations Research},
  address = {New York}
}

@ARTICLE{FORR2000,
  author = {Lucy R. Forrest and Andreas Kukol and Isaiah T. Arkin and D. Peter
	Tieleman and Mark S. P. Sansom},
  title = {Exploring models of the \mbox{Influenza A M2} channel: MD simulations
	in a phospholipid bilayer},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {55--69}
}

@ARTICLE{FRAN2000,
  author = {Harry A. Frank and James A. Bautista and Jesusa Josue and Zeus Pendon
	and Roger G. Hiller and Frank P. Sharples and David Gosztola and
	Michael R. Wasielewski},
  title = {Effect of the Solvent Environment on the Spectroscopic Properties
	and Dynamics of the Lowest Excited States of Carotenoids},
  journal = {J.~Phys.~Chem.~B},
  year = {2000},
  volume = {104},
  pages = {4569--4577}
}

@ARTICLE{FRAN2000A,
  author = {H. Frank and J. Bautista and J. Josue and A. Young},
  title = {Mechanism of nonphotochemical quenching in green plants: energies
	of the lowest excited singlet states of violaxanthin and zeaxanthin},
  journal = {Biochem.},
  year = {2000},
  volume = {39},
  pages = {2831--2837}
}

@ARTICLE{GaSh00,
  author = {Jason Gans and David Shalloway},
  title = {Shadow mass and the relationship between velocity and momentum in
	symplectic numerical integration},
  journal = PRE,
  year = {2000},
  volume = {61},
  pages = {4587--4592},
  number = {4}
}

@ARTICLE{GoWi98,
  author = {Brian B. Goldman and W. Todd Wipke},
  title = {QSD quadratic shape descriptors. 2. {M}olecular docking using quadratic
	shape descriptors (QSDock)},
  journal = PROlong,
  year = {2000},
  volume = {38},
  pages = {79--94},
  number = {1}
}

@ARTICLE{GrSS00,
  author = {A. Grama and V. Sarin and A. Sameh},
  title = {Improving Error Bounds For Multipole-Based Treecodes},
  journal = SJSC,
  year = {2000},
  volume = {21},
  pages = {1790--1803},
  number = {5}
}

@ARTICLE{GrGB00,
  author = {A. Grzybowski and E. Gwozdz and A. Brodka},
  title = {Ewald summation of electrostatic interactions in molecular dynamics
	of a three-dimensional system with periodicity in two directions},
  journal = {Phys. Rev.},
  year = {2000},
  volume = {61},
  pages = {6706--6712}
}

@INPROCEEDINGS{HaLu00,
  author = {Ernst Hairer and Christian Lubich},
  title = {Asymptotic Expansions and Backward Analysis for Numerical Integrators},
  booktitle = {Dynamics of Algorithms},
  year = {2000},
  pages = {91--106},
  address = {New York},
  organization = {{IMA} {V}ol. {M}ath. {A}ppl 118},
  publisher = {Springer-Verlag}
}

@ARTICLE{HaLu00a,
  author = {Ernst Hairer and Christian Lubich},
  title = {Long-Time Energy Conservation of Numerical Methods for Oscillatory
	Differential Equations},
  journal = SJNA,
  year = {2000},
  volume = {38},
  pages = {414--441},
  number = {2}
}

@ARTICLE{HAYA00,
  author = {S.~Hayashi and I.~Ohmine},
  title = {Proton Transfer in Bacteriorhodopsin; Structure, Excitation and {IR}
	Spectra, and Potential Energy Surface Analyses by an {\it ab initio
	} QM/MM method},
  journal = JPCB,
  year = {2000},
  note = {Submitted}
}

@ARTICLE{HEF+00,
  author = {Helmlinger, G. AND Endo, M. AND Ferrara, N. AND Hlatky, L. AND Jain,
	R. K.},
  title = {Growth factors - formation of endothelial cell networks},
  journal = {Nature},
  year = {2000},
  volume = {405},
  pages = {139--141},
  annote = {Vascular endothelial growth factor (VEGF-A) is a major regulator
	of blood vessel formation and function. it controls several processes
	in endothelial cells such as proliferation survival and migration
	but it is not known how these are coordinately regulated to result
	in more complex morphogenetic events such as tubular sprouting fusion
	and network formation. We show here that VEGF-A controls angiogenic
	sprouting in the early postnatal retina by guiding filopodial extension
	from specialized endothelial cells situated at the tips of the vascular
	sprouts. The tip cells respond to VEGF-A only by guided migration;
	the proliferative response to VEGF-A occurs in the sprout stalks.
	These two cellular responses are both mediated by agonistic activity
	of VEGF-A on VEGF receptor 2. Whereas tip cell migration depends
	on a gradient of VEGF-A proliferation is regulated by its concentration.
	Thus vessel patterning during retinal angiogenesis depends on the
	balance between two different qualities of the extracellular VEGF-A
	distribution which regulate distinct cellular responses in defined
	populations of endothelial cells. PY 2003},
  from = {INSTITUTE OF SCIENTIFIC INFORMATION:}
}

@ARTICLE{Hoge00,
  author = {P.~Hogeweg},
  title = {Shapes in the shadow: Evolutionary dynamics of morphogenesis},
  journal = {Artificial Life},
  year = {2000},
  volume = {6},
  pages = {85--101},
  number = {1}
}

@ARTICLE{Hoge00a,
  author = {P.~Hogeweg},
  title = {Evolving mechanisms of morphogenesis: on the interplay between differential
	adhesion and cell differentiation},
  journal = {J. Theor. Biol.},
  year = {2000},
  volume = {203},
  pages = {317--333},
  number = {4}
}

@ARTICLE{Hous00,
  author = {Elias~N. Houstis and Ann Christine Catlin and John R. Rice and Vassilios
	S. Verykios and Naren Ramakrishnan and Catherine E. Houstis},
  title = {{PYTHIA-II}: A Knowledge/Database System for Managing Performance
	Data and Recommending Scientific Software},
  journal = ACMTMS,
  year = {2000},
  volume = {26},
  pages = {227--253},
  number = {2},
  nremark = {A recommender example.}
}

@ARTICLE{HU2000,
  author = {Xiche Hu and Thorsten Ritz and Ana Damjanovi\'{c} and Klaus Schulten},
  title = {Photosynthetic Apparatus of Purple Bacteria},
  journal = {Quart.~Rev.~Biophys.},
  year = {2000},
  note = {In preparation}
}

@INPROCEEDINGS{IWSV00,
  author = {J.~A. Izaguirre and J.~J. Willcock and T.~S. Slabach and G.~V. Viamontes},
  title = {Object Oriented Program for Molecular Dynamics},
  booktitle = {Proc.~Midwest Numerical Analysis Day},
  year = {2000}
}

@INCOLLECTION{JAG+00,
  author = {Y.~Jiang and M.~Asipauskas and J.~A. Glazier and M.~Aubouy and F.~Graner},
  title = {{\em Ab initio} derivation of stress and strain in fluid foams},
  booktitle = {Foams, Emulsions and their Applications},
  publisher = {Verlag MIT Publishing, Bremen, Germany},
  year = {2000},
  editor = {P. Zitha and J. Banhart and G. Verbist},
  pages = {297--304}
}

@ARTICLE{BKWS00,
  author = {R. M. Brosh Jr and J. K. Karow and E. J. White and N. D. Shaw and
	I. D. Hickson and V. A. Bohr},
  title = {Potent inhibition of werner and bloom helicases by {DNA} minor groove
	binding drugs},
  journal = {Nucleic Acids Res.},
  year = {2000},
  volume = {28},
  pages = {2420--30},
  number = {12}
}

@ARTICLE{KaMi00,
  author = {M. Kawata and M. Mikami},
  title = {Computationally efficient canonical molecular dynamics simulations
	by using a multiple time-step integrator algorithm combined with
	the particle mesh {E}wald method and with the fast multipole method},
  journal = JCC,
  year = {2000},
  volume = {21},
  pages = {201--217},
  number = {3},
  annote = {An efficient implementation of the canonical molecular dynamics simulation
	using the reversible reference system propagator algorithm (r-RESPA)
	combined with the particle mesh Ewald method (PMEM) and with the
	macroscopic expansion of the fast multipole method (MEFMM) was examined.
	The performance of the calculations was evaluated for systems with
	3000, 9999, 30,000, 60,000, and 99,840 particles. For a given accuracy,
	the optimal conditions for minimizing the CPU time for the implementation
	of the Ewald method, the PMEM, and the MEFMM were first analyzed.
	Using the optimal conditions, we evaluated the performance and the
	reliability of the integrated methods. For all the systems examined,
	the r-RESPA with the PMEM was about twice as fast as the r-RESPA
	with the MEFMM. The difference arose from the difference in the numerical
	complexities of the fast Fourier transform in the PMEM and from the
	transformation of the multipole moments into the coefficients of
	the local field expansion in the MEFMM. Compared with conventional
	methods, such as the velocity-verlet algorithm with the Ewald method,
	significant speedups were obtained by the integrated methods; the
	speedup of the calculation was a function of system size, and was
	a factor of 100 for a system with 3000 particles and increased to
	a factor of 700 for a system with 99,840 particles. These integrated
	calculations are, therefore, promising for realizing large-scale
	molecular dynamics simulations for complex systems.}
}

@ARTICLE{KESS2000,
  author = {Amit Kessel and David S. Cafiso and Nir Ben-Tal},
  title = {Continuum solvent model calculations of alamethicin-membrane interactions:
	thermodynamic aspects},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {571--583}
}

@ARTICLE{KESS2000A,
  author = {Amit Kessel and Klaus Schulten and Nir Ben-Tal},
  title = {Calculations Suggest a Pathway for the Transverse Diffusion of a
	Hydrophobic Peptide Across a Lipid Bilayer},
  journal = BJ,
  year = {2000},
  volume = {79},
  pages = {2322--2330}
}

@ARTICLE{KSYD00,
  author = {K. Kholmurodov and W. Smith and K. Yasuoka and T. Darden and T. Ebisuzaki},
  title = {A smooth-particle mesh Ewald method for {DL\_POLY} molecular dynamics
	simulation package on the {F}ujitsu {VPP700}},
  journal = {Journal of Computational Chemistry},
  year = {2000},
  volume = {21},
  pages = {1187--1191},
  number = {13},
  annote = {An N log (N) smooth-particle mesh Ewald method has been incorporated
	into the DL_POLY molecular dynamics simulation package. The performance
	of the new code has been tested on a Fujitsu VPP700 for several DL_POLY-specific
	benchmark systems. The new method is highly vectorizable, and makes
	use of the extremely efficient Fast Fourier Transforms on the Fujitsu
	vector machine. In calculations of the coulombic forces in periodic
	systems requiring large reciprocal space vectors, the new code was
	found to be considerably faster than the conventional Ewald method.}
}

@ARTICLE{KLEI2000,
  author = {F. J. Kleima and E. Hofmann and B. Gobets and I. H. M. {van Stokkum}
	and R. {van Grondelle} and K. Diederichs and H. {van Amerongen}},
  title = {F\"orster Excitation Energy Transfer in Peridinin-Chlorophyll-{\em
	a}-Protein},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {344--353}
}

@ARTICLE{KLEI2000A,
  author = {F. J. Kleima and M. Wendling and E. Hofmann and E. J. G. Peterman
	and R. {van Grondelle} and H. {van Amerongen}},
  title = {Peridinin chlorophyll {\em a} protein: relating structure and steady-state
	spectroscopy},
  journal = BCH,
  year = {2000},
  volume = {39},
  pages = {5184--5195},
  number = {17}
}

@ARTICLE{Kome00,
  author = {Y. Komeiji},
  title = {Ewald summation and multiple time step methods for molecular dynamics
	simulation of biological molecules},
  journal = {Journal of Molecular Structure (THEOCHEM)},
  year = {2000},
  volume = {530},
  pages = {237--243},
  number = {3},
  annote = {Methods by which to determine conditions for a molecular dynamics
	(MD) simulation of biological molecules were investigated. Derivation
	of the optimal parameters of the Ewald summation was described so
	as to give same precision to the real space, the reciprocal space
	summations and the van der Waals interaction. Later, the procedure
	by which to determine the condition of the multiple time step method
	by RESPA (REference System Propagator Algorithm; Tuckerman et al.,
	1992, J. Chem. Phys., 97, 1990) was described as exemplified by MD
	simulations of a solvated -sheet peptide. The conservation of the
	total energy in a microcanonical ensemble was measured to investigate
	the stability of the simulation conditions. The most feasible respective
	combinations of the time steps were: 0.25 fs for bond, angle and
	torsion interactions; 2 fs for van der Waals interaction and Ewald
	real-space summation; and 4 fs for Ewald reciprocal-space summation.
	Though it retained an acceptable accuracy, this condition accelerated
	the simulation ten-fold compared to that in which a simple velocity-Verlet
	method with a time step of 0.25 fs was used. The update of the correction
	term due to excluded neighbors was then investigated. Better results
	were obtained when the correction was updated with the real-space
	than when it was updated with the reciprocal-space summation. Finally,
	an MD simulation as long as 50 ps performed under the optimal Ewald
	and RESPA parameters was thus determined. The trajectory showed a
	good stability, indicating the feasibility of the parameters.}
}

@ARTICLE{KRUE00,
  author = {Brent P. Krueger and Stefania S. Lampoura and Ivo H. M. van Stokkum
	and Jante M. Salverda and Claudiu C. Gradinaru and Danielis Rutkauskas
	and Roger G. Hiller and Rienk van Grondelle},
  title = {A Polarized Transient Absorption Study of Energy Transfer in the
	Peridinin Chlorophyll-{\em a} Protein of {{\em Amfidinium carterae}}},
  journal = BJ,
  year = {2000},
  note = {submitted}
}

@ARTICLE{LaTu00,
  author = {L. J. LaBerge and J. C. Tully},
  title = {A Rigorous Procedure for Combining Molecular Dynamics and {M}onte
	{C}arlo Simulation Algorithms},
  journal = CP,
  year = {2000},
  volume = {260},
  pages = {183--191},
  number = {1-2},
  abstract = {A combination of molecular dynamics (MD) and {M}onte {C}arlo (MC)
	simulation methods is proposed that may have advantages in some cases
	over either MD or MC alone. The method is simple: in each step of
	the algorithm, some of the particles are moved by MC rules and the
	rest by MD. We prove that the mixed method converges rigorously to
	the same equilibrium state as either MC or canonical MD alone; i.e.,
	the sudden interruption of forces produced by the MC moves does not
	incorrectly bias the evolution of the MD particles. The method is
	tested on a simulation of a Lennard-Jones fluid. The results confirm
	that the mixed method (MDMC) achieves the correct statistics and
	that the overhead associated with the mixed methods is modest. MDMC
	may be more efficient than either MD or MC for simulating molecular
	systems in which some degrees of freedom are more effectively treated
	by MC (e.g., solvent motions) and others by MD (e.g., hydrocarbon
	chains).},
  annote = {dihedral moves - pointed out by Mark Lipton, Chemistry, Purdue}
}

@ARTICLE{Lent00,
  author = {Craig S. Lent},
  title = {Molecular Electronics: Bypassing the Transistor Paradigm},
  journal = SCI,
  year = {2000},
  volume = {288},
  pages = {1597--1599}
}

@ARTICLE{LEUP2000,
  author = {D. Leupold and B. Voigt and W. Beenken and H. Stiel},
  title = {Pigment-protein architecture in the light-harvesting antenna complexes
	of purple bacteria: does the crystal structure reflect the native
	pigment-protein arrangement?},
  journal = {FEBS Letters},
  year = {2000},
  volume = {480},
  pages = {73--78}
}

@ARTICLE{LIN2000,
  author = {Jung-Hsin Lin and A. Baumgaertner},
  title = {Stability of a melittin pore in a lipid bilayer: a molecular dynamics
	study},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {1714--1724}
}

@INCOLLECTION{LU2000A,
  author = {Hui Lu and Andr{\'e} Krammer and Barry Isralewitz and Viola Vogel
	and Klaus Schulten},
  title = {Computer modeling of force-induced titin domain unfolding},
  booktitle = {Elastic Filaments of the Cell},
  publisher = {Kluwer Acaddemic/Plenum Publishers},
  year = {2000},
  editor = {Jerry Pollack and Henk Granzier},
  chapter = {1},
  pages = {143--162},
  address = {New York, NY}
}

@ARTICLE{LU2000,
  author = {Hui Lu and Klaus Schulten},
  title = {The Key Event in Force-Induced Unfolding of Titin's Immunoglobulin
	Domains},
  journal = BJ,
  year = {2000},
  volume = {79},
  pages = {51--65}
}

@ARTICLE{LyLa00,
  author = {A.~P. Lyubartsev and A. Laaksonen},
  title = {{MD}yna{M}ix -- A scalable portable parallel {MD} simulation package
	for arbitrary molecular mixtures},
  journal = CPC,
  year = {2000},
  volume = {128},
  pages = {565--589},
  annote = {MDynaMix,http://www.fos.su.se/physical/sasha/md_prog.html}
}

@ARTICLE{MSXK00,
  author = {J.~Ma and P.~B.~Sigler and Z.~Xu and M.~Karplus},
  title = {A dynamic model for the allosteric mechanism of GroEL},
  journal = JMB,
  year = {2000},
  volume = {302},
  pages = {303--313}
}

@ARTICLE{MaTs00,
  author = {G. Marsaglia and W.W. Tsang},
  title = {The ziggurat method for generating random variables},
  journal = {Journal of Statistical Software},
  year = {2000},
  volume = {5},
  pages = {1--7},
  number = {8}
}

@INBOOK{MvHA00,
  chapter = {6},
  pages = {177--195},
  title = {Biochemistry},
  publisher = {Addison Wesley},
  year = {2000},
  author = {C.~K. Mathews and K.~E. van Holde and K.~G. Ahern},
  edition = {Third}
}

@ARTICLE{MAUR2000,
  author = {Joshua A. Maurer and Donald E. Elmore and Henry A. Lester and Dennis
	A. Dougherty},
  title = {Comparing and contrasting {\it {Escherichia} coli} and {\it {Mycobacterium}
	tuberculosis} mechanosensitive channels ({MscL})},
  journal = JBC,
  year = {2000},
  volume = {275},
  pages = {22238--22244},
  number = {29}
}

@BOOK{MAY2000,
  title = {Charge and Energy Transfer Dynamics in Molecular Systems},
  publisher = {WILEY-VCH},
  year = {2000},
  author = {Volkhard May and Oliver K{\"u}hn},
  address = {Verlag GmbH, Berlin (Federal Republic of Germany)}
}

@ARTICLE{Mcdo00,
  author = {Tim McDonald},
  title = {Intel Announces Super-Fast Transistors: Intel's new transistors are
	the stuff of science fiction, proving that science is far from hitting
	the speed wall},
  journal = {NewsFactor Network},
  year = {2000},
  note = {Available online at http://www.newsfactor.com/perl/story/5970.html},
  annote = {Intel Announces Super-Fast Transistors By Tim McDonald NewsFactor
	Network December 11, 2000 Intel's new transistors are the stuff of
	science fiction, proving that science is far from hitting the speed
	wall. Intel Corp. (Nasdaq: INTC) researchers say they have developed
	the world's smallest and fastest transistors, with architectures
	almost as small as human DNA and capable of allowing computer processors
	to complete 400 million calculations literally in the blink of an
	eye. The technological breakthrough, Intel officials say, will allow
	processor speeds to increase tenfold over the next five years. Transistors
	control the speed and efficiency of processors; the more transistors,
	the faster, more efficient and sophisticated the chip. Intel's new
	CMOS transistor is 30 nanometers and three atomic layers thick: more
	than 100,000 would be needed to achieve the thickness of a single
	sheet of paper. Moore's Law Intel co-founder Gordon Moore thought
	up his famous "Moore's Law" a generation ago, when Intel?s first
	microprocessor chip, the 4004, offered only 2,300 calculations over
	a much larger footprint. Moore's Law stated that, as the size of
	transistors shrink, the number of transistors contained on a given
	chip would double every 18 to 24 months. However, Moore himself had
	doubts whether this trend would continue once transistor size shrunk
	to 0.25 microns. Intel researchers now say their goal is to shrink
	their processors' transistors by 30 percent every two years. "It's
	discoveries like these that make me excited about the future," general
	manager of Intel's Technology and Manufacturing Group, Sunlin Chou,
	told reporters. "It's one thing to achieve a great technological
	breakthrough. It's another to have one that is practical and will
	change everyone's lives." The company will reveal more details on
	the transistors later today at the International Electron Devices
	Meeting in San Francisco. No Barriers The announcement implies that
	there are no known physical barriers to increasing chip speed for
	at least the next five to 10 years, though many experts believe that
	science will hit a wall at some undetermined point in the future.
	The new technology will allow chips to contain 400 million of these
	transistors and run at 10 gigahertz. A 10 GHz processor can complete
	20 million calculations in the time a speeding bullet travels a foot,
	bringing to reality computing possibilities that have previously
	been in the realm of science fiction. For example, it would make
	possible real-time voice translation, like the universal translator
	seen on Star Trek. Little Power Required Currently Intel's most powerful
	processors, the Pentium 4 and the upcoming 64-bit Itanium, employ
	0.18 micron technology. Intel engineers plan to increase that to
	0.13 microns by the end of next year, when they will switch from
	aluminum to copper in their transistor relays. That speed will be
	increased to 0.10 with the goal of reaching 0.07. The 10 GHz chip
	that Intel hopes to be producing by 2005 will require less than one
	volt. The Pentium 4 chip runs at 1.5 GHz and contains 42 million
	transistors. "Many experts thought it would be impossible to build
	CMOS transistors this small," director of Intel's Components Research
	Lab Gerald Marcyk told reporters. "Our research proves that there
	are no fundamental barriers to producing these devices in high volumes
	in the future."}
}

@BOOK{McQu00,
  title = {Statistical Mechanics},
  publisher = {University Science Books},
  year = {2000},
  author = {Donald A. McQuarrie},
  address = {Sausalito, CA},
  edition = {2nd}
}

@ARTICLE{MiSh00,
  author = {T. Miura and K. Shiota},
  title = {{T}{G}{F}-{B}eta 2 Acts As an ``Activator'' Molecule in Reaction-Diffusion
	Model and Is Involved in Cell Sorting Phenomenon in Mouse Limb Micromass
	Culture},
  journal = {Developmental Dynamics},
  year = {2000},
  volume = {217},
  pages = {241--249},
  number = {3}
}

@ARTICLE{MOLN2000A,
  author = {Ferenc Molnar and Michal Ben-Nun and Todd J. {Mart{\'{\i}}nez} and
	Klaus Schulten},
  title = {Characterization of a Conical Intersection between the Ground and
	First Excited State for a Retinal Analog},
  journal = {Journal of Molecular Structure (THEOCHEM)},
  year = {2000},
  volume = {{WATOC} special issue, 506},
  pages = {169--178}
}

@ARTICLE{MOLN2000,
  author = {Ferenc Molnar and Lawrence S. Norris and Klaus Schulten},
  title = {Simulated Unbinding and Binding of Fatty Acid Substrates in the Cyclooxygenase
	Site of Prostaglandin {H$_{2}$} Synthase-1},
  journal = {Progress in Reaction Kinetics and Mechanisms},
  year = {2000},
  volume = {25},
  pages = {263--298}
}

@ARTICLE{MOOR2000,
  author = {Moore, D. B. and Martinez, T. J.},
  title = {Ab Initio Study of Coupled Electron Transfer/Proton Transfer in Cytrochrome
	c Oxidase},
  journal = JPC,
  year = {2000},
  volume = {104A},
  pages = {2367},
  abstract = {The coupled electron/proton transfer mechanism of cytochrome c oxidase
	is investigated using ab initio electronic structure theory. We predict
	the location and identity of the Fe and Cu ligands in the oxidized
	(O), partially reduced (E), and fully reduced (R) forms of the enzyme.
	Our calculations suggest that a tyrosine residue in close proximity
	to the active site is deprotonated during the enzymatic cycle. These
	predictions are consistent with experimental evidence and provide
	a molecular explanation for both the observed antiferromagnetic coupling
	of Fe(3+) and Cu(2+) and the distinction between "fast" and "slow"
	forms of the oxidized enzyme.}
}

@INPROCEEDINGS{MNKI00,
  author = {Richard Murphy and Mike Niemier and Shannon Kuntz and J.~A. Izaguirre
	and Peter Kogge},
  title = {How Can the Protein Folding Problem be Mapped onto a Million-Processor
	PIM Array to Achieve Petaflop Performance?},
  booktitle = {Proceedings of the SIAM Annual Meeting},
  year = {2000},
  organization = {SIAM},
  note = {Session CP16, Computational Biology}
}

@ARTICLE{NAGA2000,
  author = {H. Nagae and M. Kuki and J.-P. Zhang and T. Sashima and Y. Mukai
	and Y. Koyama},
  title = {Vibronic coupling through the In-Phase, {C}={C} Stretching Mode plays
	a major role in the 2A$_g^-$-to - 1A$_g^-$ Internal Conversion of
	All-{\em trans}-$\beta$-carotene},
  journal = {J.~Phys.Chem.~A},
  year = {2000},
  volume = {104},
  pages = {4155--4166}
}

@ARTICLE{Najm00,
  author = {R. Najmanovich and J. Kuttner and V. Sobolev and M. Edelman},
  title = {Side-Chain Flexibility in Proteins Upon Ligan Binding},
  journal = {Proteins: Structure, Function, and Genetics},
  year = {2000},
  volume = {39},
  pages = {261--268}
}

@ARTICLE{NeFD00,
  author = {J. P. Neirotti and David L. Freeman and J. D. Doll},
  title = {Approach to ergodicity in {M}onte {C}arlo simlations},
  journal = PRE,
  year = {2000},
  volume = {65},
  pages = {7445--7461},
  number = {5}
}

@ARTICLE{NyLi00,
  author = {T. M. Nymand and P. Linse},
  title = {Ewald summation and reaction field methods for potentials with atomic
	charges, dipoles, and polarizabilities},
  journal = {J. Chem. Phys.},
  year = {2000},
  volume = {112},
  pages = {6152--6160}
}

@ARTICLE{OOPP00,
  author = {P.M. O'Brien and D.F. Ortwine and A.G. Pavlovsky and J.A. Picard
	and D.R. Sliskovic and B.D. Roth and R. Dyer and L. Johnson and C.F.
	Man and H. Hallak},
  title = {Structure Activity Relationships and Pharmacokinetic Analysis For
	a Series of Potent, Systemically Available Biphenyl Sulfonamide Matrix
	Metalloproteinase ({MMP}) Inhibitors},
  journal = JMC,
  year = {2000},
  volume = {43},
  pages = {156--166}
}

@ARTICLE{OPLM00,
  author = {B. C. Oostenbrink and J. W. Pitera and M. M. H. van Lipzig and J.
	H. N. Meerman and W. F. van Gunsteren},
  title = {Simulation of the estrogen receptor ligand-binding domain: affinity
	of natural ligands and xenoestrogens},
  journal = JMC,
  year = {2000},
  volume = {43},
  pages = {4594--4605}
}

@ARTICLE{PaMO00,
  author = {K. J. Painter and P. K. Maini and H. G. Othmer},
  title = {A chemotactic model for the advance and retreat of the primitive
	streak in avian development.},
  journal = {Bulletin of Mathematical Biology},
  year = {2000},
  volume = {217},
  pages = {501--525}
}

@MISC{PYMP00,
  author = {PyMPI},
  title = {An Introduction to Parallel Python using MPI},
  howpublished = {\url{http://sourceforge.net/projects/pympi/}},
  year = {2000},
  annote = {PyMPI Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{PANK2000,
  author = {Oliver P{\"a}nke and Karin Gumbiowski and Wolfgang Junge and Siegfried
	Engelbrecht},
  title = {F-ATPase: specific observation of the rotating c subunit oligomer
	of EF$_0$EF$_1$},
  journal = FEBS,
  year = {2000},
  volume = {472},
  pages = {34--38}
}

@ARTICLE{Refs00,
  author = {K. Refson},
  title = {Moldy: {A} portable molecular dynamics simulation program for serial
	and parallel computers},
  journal = CPC,
  year = {2000},
  volume = {126},
  pages = {309--328},
  number = {3},
  annote = {MOLDY: http://www.earth.ox.ac.uk/~keith/moldy.html}
}

@ARTICLE{RUG+00,
  author = {J.~P. Rieu and A.~Upadhyaya and J.~A. Glazier and B.~O. Noryuki and
	Y.~Sawada},
  title = {Diffusion and deformations of single {\em Hydra} cells in cellular
	aggregates},
  journal = {Biophys.\ J.},
  year = {2000},
  volume = {79},
  pages = {1903--1914},
  number = {4}
}

@ARTICLE{RITZ2000,
  author = {Thorsten Ritz and Salih Adem and Klaus Schulten},
  title = {A Model for Vision-Based Magnetoreception in Birds},
  journal = BJ,
  year = {2000},
  volume = {78},
  number = {2},
  note = {In press.}
}

@ARTICLE{RITZ2000B,
  author = {Thorsten Ritz and Ana Damjanovi\'{c} and Richard Cogdell and Thomas
	Gillbro and Klaus Schulten},
  title = {Carotenoid-Chlorophyll Transfer in {LH2} from {{\em Rhodopseudomonas
	acidophila}}},
  journal = JPC,
  year = {2000}
}

@ARTICLE{RoGT00,
  author = {J. Roth and F. G{\"a}hler and H.-R. Trebin},
  title = {A molecular dynamics run with 5.180.116.000 particles},
  journal = IJMPC,
  year = {2000},
  volume = {11},
  pages = {317--322},
  number = {2}
}

@ARTICLE{SASH2000,
  author = {T. Sashima and Y. Koyama and T. Yamada and H. Hashimoto},
  title = {The 1B$_u^-$ and 2A$_g^-$ energies of lycopene, $\beta$-carotene
	and Mini-9-$\beta$-carotene as determined by resonance-{R}aman excitation
	profile: Dependence of the 1B$_u^-$-state energy on the conjugation
	length},
  journal = {J.~Phys.~Chem.~B},
  year = {2000},
  volume = {104},
  pages = {5011--5019}
}

@ARTICLE{SCHU2000,
  author = {Klaus Schulten},
  title = {Electron transfer: {Exploiting} Thermal Motion},
  journal = SCI,
  year = {2000},
  volume = {290},
  pages = {61--62},
  annote = {Invited article, published in the "Perspectives" section of "Science".}
}

@ARTICLE{SCHU2000A,
  author = {Klaus Schulten},
  title = {To Students Contemplating Research in Biomolecular Modelling},
  journal = {Journal of Molecular Graphics and Modeling},
  year = {2000},
  volume = {18},
  pages = {218--220}
}

@BOOK{SCOT00,
  title = {Programming Language Pragmatics},
  publisher = {Academic Press},
  year = {2000},
  author = {M.~L. Scott},
  address = {San Diego}
}

@ARTICLE{SGI,
  author = {SGI},
  title = {The Great Leap Forward in Molecular Structure Simulation and Modeling},
  journal = {http://www.sgi.com/features/1999/mar/chemistry/index.html},
  year = {2000}
}

@ARTICLE{SCTW00,
  author = {Yuk Yin Sham and Zhen Tao Chu and Holly Tao and Arieh Warshel},
  title = {Examining methods for calculations of binding free energies: {LRA,LIE,PDLD-LRA,}
	and {PDLD/S-LRA} calculations of ligands binding to an {HIV} protease},
  journal = PROlong,
  year = {2000},
  volume = {39},
  pages = {393--407},
  number = {4}
}

@ARTICLE{SHAR2000,
  author = {Rajeev Sharma and Michael Zeller and Vladimir I. Pavlovic and Thomas
	S. Huang and Zion Lo and Stephen Chu and Yunxin Zhao and James C.
	Phillips and Klaus Schulten},
  title = {Speech/Gesture Interface to a Visual-Computing Environment},
  journal = {IEEE Computer Graphics and Applications},
  year = {2000},
  volume = {20},
  pages = {29--37}
}

@ARTICLE{SHRI2000,
  author = {Indira H. Shrivastava and Mark. S. P. Sansom},
  title = {Simulations of ion permeation through a potassium channel: {M}olecular
	dynamics of {KcsA} in a phospholipid bilayer},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {557--570}
}

@ARTICLE{SiBe00,
  author = {E. G. Sirer and B. N. Bershad},
  title = {Using Production Grammars in Software Testing},
  journal = {ACM Sigplan Notices},
  year = {2000},
  volume = {35},
  pages = {1--13},
  number = {1}
}

@ARTICLE{SkHM00,
  author = {I. Skauvik and J.~P. Hansen and T. Matthey},
  title = {Dynamics of clustering in a binary {L}ennard-{J}ones material},
  journal = {Modelling Simul. Mater. Sci. Eng.},
  year = {2000},
  volume = {8},
  pages = {665--676},
  number = {5},
  annote = {We have performed constant temperature two-dimensional molecular
	dynamics simulations of a binary Lennard-Jones material, representing
	an idealized metallic alloy or a material containing a specified
	fraction of an additive atomic species. Differences in the interatomic
	potentials between the atomic species can lead to clustering of the
	alloy atoms. An exponential distribution of cluster size is obtained
	as time approaches infinity. For sufficiently strong attractions
	the distribution of cluster sizes becomes nearly independent of the
	force and the attained maximum cluster size reaches a saturation
	level.}
}

@ARTICLE{SkSr00,
  author = {R.~D. Skeel and K. Srinivas},
  title = {Nonlinear Stability Analysis of Area-Preserving Integrators},
  journal = SJNA,
  year = {2000},
  volume = {38},
  pages = {129--148},
  number = {1}
}

@ARTICLE{SuKO00,
  author = {Yuji Sugita and Akio Kitao and Yuko Okamoto},
  title = {Multidimensional replica-exchange method for free-energy calculations},
  journal = JCP,
  year = {2000},
  volume = {113},
  pages = {6042--6051},
  number = {15}
}

@INPROCEEDINGS{Sutm00,
  author = {G. Sutmann},
  title = {Classical Dynamics},
  booktitle = {Quantum Simulations of Complex Many-Body Systems: From Theory to
	Algorithms},
  year = {2000},
  editor = {J. Grotendorst and D. Marx and A. Muramatsu},
  volume = {10},
  series = {NIC},
  pages = {211--254},
  address = {Forschungszentrum J{\"u}lich, Germany},
  organization = {John von Neumann Institute for Computing},
  publisher = {NIC-Directors}
}

@BOOK{Sutt00,
  title = {Exceptional {C\texttt{++}}: 47 Engineering Puzzles, Programming Problems,
	and Solutions},
  publisher = {Addison-Wesley},
  year = {2000},
  author = {H. Sutter}
}

@BOOK{Sutt02,
  title = {More Exceptional {C\texttt{++}}: 40 New Engineering Puzzles, Programming
	Problems, and Solutions},
  publisher = {Addison-Wesley},
  year = {2000},
  author = {H. Sutter}
}

@ARTICLE{TAJK2000,
  author = {Emad Tajkhorshid and Jerome Baudry and Klaus Schulten and Sandor
	Suhai},
  title = {Molecular dynamics study of the nature and origin of retinal's twisted
	structure in bacteriorhodopsin},
  journal = BJ,
  year = {2000},
  volume = {78},
  pages = {683--693},
  number = {2}
}

@ARTICLE{TSBD00,
  author = {A. Toukmaji and C. Sagui and J. Board and T. Darden},
  title = {Efficient particle-mesh {E}wald based approach to fixed and induced
	dipolar interactions},
  journal = JCP,
  year = {2000},
  volume = {113},
  pages = {10913--10927},
  number = {24},
  annote = {We have implemented classical Ewald and particle-mesh Ewald (PME)
	based treatments of fixed and induced point dipoles into the sander
	molecular dynamics (MD) module of AMBER 6. During MD the induced
	dipoles can be propagated along with the atomic positions either
	by iteration to self-consistency at each time step, or by a Car-Parrinello
	(CP) technique using an extended Lagrangian formalism. In this paper
	we present the derivation of the new algorithms and compare the various
	options with respect to accuracy, efficiency, and effect on calculated
	properties of a polarizable water model. The use of PME for electrostatics
	of fixed charges and induced dipoles together with a CP treatment
	of dipole propagation in MD simulations leads to a cost overhead
	of only 33\% above that of MD simulations using standard PME with
	fixed charges, allowing the study of polarizability in large macromolecular
	systems.}
}

@ARTICLE{TYSH00,
  author = {Mark E. Tuckerman and D.A. Yarne and Shane O. Samuelson and Adam
	L. Hughes and Glenn J. Martyna},
  title = {Exploiting multiple levels of parallelism in molecular dynamics based
	calculations via modern techniques and software paradigms on distributed
	memory computers},
  journal = CPC,
  year = {2000},
  volume = {128},
  pages = {333--376}
}

@PHDTHESIS{Upad00,
  author = {A. Upadhyaya},
  title = {Thermodynamic and fluid properties of cells, tissues and membranes},
  school = {University of Notre Dame, USA},
  year = {2000}
}

@TECHREPORT{Veld00,
  author = {T. Veldhuizen},
  title = {Techniques for Scientific {C\texttt{++}}},
  institution = {Indiana University Computer Science Department},
  year = {2000},
  number = {542}
}

@MISC{W3C00,
  author = {W3C},
  title = {W3C XML Schema},
  year = {2000},
  note = {\url{http://www.w3.org/XML/}}
}

@ARTICLE{WALL2000,
  author = {Peter J. Walla and Jenny Yom and Brent P. Krueger and Graham R. Fleming},
  title = {Two-Photon Excitation Spectrum of Light-Harvesting Complex {II} and
	Fluorescence Upconversion after One- and Two-Photon Excitation of
	the Carotenoids},
  journal = {J.~Phys.~Chem.~B},
  year = {2000},
  volume = {104},
  pages = {4799--4806}
}

@ARTICLE{WEAV2000,
  author = {J.C. Weaver and T.E. Vaughan and R.D. Astumian},
  title = {Biological sensing of small field differences by magnetically sensitive
	chemical reactions},
  journal = NAT,
  year = {2000},
  volume = {405},
  pages = {707--709}
}

@ARTICLE{WeHM00,
  author = {W. Weber and P. H. H\"unenberger and J. A. McCammon},
  title = {MOLECULAR DYNAMICS SIMULATIONS OF A POLYALANINE OCTAPEPTIDE UNDER
	EWALD BOUNDARY CONDITIONS: INFLUENCE OF ARTIFICIAL PERIODICITY ON
	PEPTIDE CONFORMATION},
  journal = JPCB,
  year = {2000},
  volume = {104},
  pages = {3668--3675},
  abstract = { Ewald and related mesh methods are nowadays routinely used in explicit-solvent
	simulations of solvated biomolecules, although they impose an artificial
	periodicity in systems which are inherently non-periodic. In the
	present study, we investigate the consequences of this approximation
	for the conformational equilibrium of a polyalanine octapeptide (with
	charged termini) in water. We report three explicit-solvent molecular
	dynamics simulations of this peptide in cubic unit cells of edges
	L = 2, 3 and 4 nm, using the particle-particle-particle mesh (P^3M)
	method for handling electrostatic interactions. The initial configuration
	of the peptide is alpha-helical. In the largest unit cell (L = 4
	nm), the helix unfolds quickly towards configurations with shorter
	end-to-end distances. By contrast, in the two smaller unit cells
	(L = 2 and L =3 nm), the alpha-helix remains stable during two nanoseconds.
	Backbone fluctuations are somewhat larger in the medium (L = 3 nm)
	compared to the smallest unit cell. These differences are rationalized
	using a continuum electrostatic analysis of configurations from the
	simulations. These calculations show that the alpha-helical conformation
	is stabilized by artificial periodicity relative to any other configuration
	sampled during the trajectories. This artificial stablilization is
	larger for smaller unit cells, and is responsible for the absence
	of unfolding in the two smaller unit cells and the reduced backbone
	fluctuations in the smallest unit cell. These results suggest that
	artificial periodicity imposed by the use of infinite periodic (Ewald)
	boundary conditions in explicit-solvent simulations of biomolecules
	may significantly perturb the potentials of mean force for conformational
	equilibria, and even in some cases invert the relative stabilities
	of the folded and unfolded states. }
}

@ARTICLE{WEBE2000,
  author = {Wolf-Michael Weber and Christian Popp and Wolfgang Clauss and Willy
	Van Driessche},
  title = {Maitotoxin induces insertion of different ion channels into the {\it
	Xenopus} oocyte plasma membrane via {Ca}$^{2+}$- stimulated exocytosis},
  journal = {Eur.\ J.\ Physiol.},
  year = {2000},
  volume = {439},
  pages = {363--369}
}

@ARTICLE{SAMD2,
  author = {Jeremiah Willcock},
  title = {SAMD2: A Molecular Dynamics Simulator Using Blitz++},
  journal = {Proceedings of CSE598E, University of Notre Dame},
  year = {2000}
}

@ARTICLE{Yoko00,
  author = {Jun Yokota},
  title = {Tumor progression and metastasis},
  journal = {Carcinogenesis},
  year = {2000},
  volume = {21},
  pages = {497--503},
  number = {3}
}

@ARTICLE{Zaja00,
  author = {M.~Zajac and G.~L. Jones and J.~A. Glazier},
  title = {Model of convergent extension in animal morphogenesis},
  journal = {Phys. Rev. Lett.},
  year = {2000},
  volume = {85},
  pages = {2022--2025},
  number = {9}
}

@ARTICLE{ZHAN00,
  author = {J.-P. Zhang and R. Fujii and P. Qian and T. Inaba and T. Mizoguchi
	and Y. Koyama},
  title = {Mechanism of the carotenoid-to-bacteriochlorophyll energy transfer
	via the {S}$_1$ state in the {LH}2 complexes from purple bacteria},
  journal = JPCB,
  year = {2000},
  volume = {104},
  pages = {3683--3691},
  number = {15}
}

@ARTICLE{ZHAN2000,
  author = {J.-P. Zhang and R. Fujii and P. Qian and T. Inaba and T. Mizoguchi
	and Y. Koyama},
  title = {Mechanism of the carotenoid-to-bacteriochlorophyll energy transfer
	via the S$_1$ state in the LH2 complexes from purple bacteria},
  journal = {J.~Phys.~Chem.~B},
  year = {2000},
  volume = {104},
  pages = {3683--3691}
}

@MISC{LaTe99,
  author = {LaTeX3},
  title = {LaTex News, Issue 12},
  howpublished = {\url{http://www.latex-project.org/ltnews/ltnews12.pdf}},
  month = DEC,
  year = {1999},
  readme = {Requires \usepackage{url} in the preamble.}
}

@BOOK{LMBB99,
  title = {Molecular Cell Biology},
  publisher = {W. H. Freeman Company},
  year = {1999},
  author = {H. Lodish and P. Matsudaira and D. Baltimore and A. Berk and L. Zipursky},
  month = NOV
}

@INPROCEEDINGS{WLKP99,
  author = {Z. Wang and J. Lupo and A. McKenney and R. Pachter},
  title = {Large Scale Molecular Dynamics Simulations With Fast Multipole Implementations},
  booktitle = {Proceedings of Supercomputing~'99},
  year = {1999},
  address = {Portland, Oregon},
  month = NOV
}

@MANUAL{Hard99,
  title = {Molecular Dynamics {API}},
  author = {D. Hardy},
  organization = {Theoretical Biophysics Group, University of Illinois at Urbana-Champaign},
  address = {405 North Matthews Avenue, Urbana, IL 61801},
  edition = {0.96},
  month = OCT,
  year = {1999},
  note = {Download at {\small \texttt{http://www.ks.uiuc.edu/\~{}dhardy/mdapi}}},
  annote = {User's manual and programmer's guide for the MDAPI.}
}

@PHDTHESIS{KLEI99,
  author = {Foske Kleima},
  title = {Light-Harvesting and Excitation Energy Transfer in Oxygenic Photosynthesis},
  school = {Vrije Universiteit},
  year = {1999},
  address = {Amsterdam},
  month = OCT
}

@MISC{ALSV99,
  author = {N. Attig and M. Lewerenz and G. Sutmann and R. Vogelsang},
  title = {{DMMD} -- {A} Modular Molecular Dynamics Program for {MPP}-Systems},
  howpublished = {5th SGI/Cray MPP Workshop, Bologna, Italy, \texttt{\small http://www.cineca.it/mpp-workshop}},
  month = SEP,
  year = {1999}
}

@MISC{MODL99,
  author = {{M}o{D}{L}},
  title = {{M}olecular {D}ynamics {Markup} {L}anguage},
  howpublished = {\url{http://xml.coverpages.org/modl.html}},
  month = AUG,
  year = {1999},
  annote = {MoDL Cover Page},
  readme = {Requires \usepackage{url} in the preamble.}
}

@INCOLLECTION{BoKL99,
  author = {N.~P. Boghossian and O. Kohlbacher and H.-P. Lenhof},
  title = {{BALL:} {B}iochemical {A}lgorithms {L}ibrary},
  booktitle = {3rd Int. Workshop on Algorithm Engineering (WAE-99)},
  publisher = {Springer-Verlag},
  year = {1999},
  editor = {J.~S Vitter and C.~D. Zaroliagis},
  volume = {1668},
  series = {Lecture Notes in Computer Science},
  pages = {330--344},
  address = {London},
  month = JUL
}

@TECHREPORT{Schu99,
  author = {C. Sch{\"u}tte},
  title = {Conformational Dynamics: Modelling, Theory, Algorithm, and Application
	to Biomolecules},
  institution = {Konrad-\-Zuse-\-Zentrum f\"ur Informationstechnik Berlin},
  year = {1999},
  month = JUL,
  note = {{SC} 99-18}
}

@ARTICLE{OIJE99,
  author = {A. M. {van Oijen} and M. Katelaars and J. K{\"o}hler and T. J. Aartsma
	and J. Schmidt},
  title = {Unraveling the Electronic Structure of Individual Photosynthetic
	Pigment-Protein Complexes},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {400--402}
}

@ARTICLE{VANB99,
  author = {M. E. {van Brederode} and R. {van Grondelle}},
  title = {New and unexpected routes for ultrafast electron transfer in photosynthetic
	reaction centers},
  journal = FEBS,
  year = {1999},
  volume = {455},
  pages = {1--7}
}

@ARTICLE{AgLA99,
  author = {D. Agnusdei and S. Liu-Leage and B. Augendre-Ferrante},
  title = {Results of international clinical trials with raloxifene},
  journal = {Ann Endocrinol (Paris)},
  year = {1999},
  volume = {60},
  pages = {242--246},
  number = {3},
  annote = {In French}
}

@ARTICLE{AlKC99,
  author = {T. W. Allen and S. Kuyucak and S. Chung},
  title = {Molecular Dynamics Study of the {K}cs{A} Potassium Channel},
  journal = {Biophysics Journal},
  year = {1999},
  volume = {77},
  pages = {2502--2516}
}

@BOOK{LaUG99,
  title = {{LAPACK} Users' Guide},
  publisher = {Society for Industrial and Applied Mathematics},
  year = {1999},
  author = {Anderson, E. and Bai, Z. and Bischof, C. and Blackford, S. and Demmel,
	J. and Dongarra, J. and Du Croz, J. and Greenbaum, A. and Hammarling,
	S. and McKenney, A. and Sorensen, D.},
  address = {Philadelphia, PA},
  edition = {Third},
  isbn = {0-89871-447-8 (paperback)}
}

@ARTICLE{BALA99,
  author = {Alexander Balaeff and L. Mahadevan and Klaus Schulten},
  title = {Elastic rod model of a {DNA} loop in the {\it lac} operon},
  journal = PRL,
  year = {1999},
  volume = {83},
  pages = {4900--4903},
  number = {23},
  annote = {Prof. Mahadevan prefers to be cited as "L. Mahadevan" rather than
	under his full name Lakshminarayan; The paper was published on December
	6}
}

@ARTICLE{BASS99,
  author = {R. Bassi and R. Croce and D. Cugini and D. Sandona},
  title = {Mutational analysis of a higher plant antenna protein provides identification
	of chromophores bound into multiple sites},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1999},
  volume = {96},
  pages = {10056--10061}
}

@ARTICLE{BAUD99,
  author = {J.~Baudry and S.~Crouzy and B.~Roux and J.C.~Smith},
  title = {Simulation Analysis of the Retinal Conformational Equilibrium in
	Dark-Adapted Bacteriorhodopsin},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {1909--1917}
}

@ARTICLE{BAUT99A,
  author = {J. A. Bautista and R. E. Connors and B. B. Raju and R. G. Hiller
	and F. P. Sharples and D. Gosztola and M. Wasielewski and H. A. Frank},
  title = {Exited State Properties of Peridinin: Observation of Solvent Dependence
	of the Lowest Excited Singlet State Lifetime and Spectral Behavior
	Unique among Carotenoids},
  journal = JPCB,
  year = {1999},
  volume = {103},
  pages = {8751--8758}
}

@ARTICLE{BAUT99,
  author = {J. A. Bautista and R. G. Hiller and F. P. Sharples and D. Gosztola
	and M. Wasielewski and H. A. Frank},
  title = {Singlet and Triplet Energy Transfer in the Peridinin-Chlorophyll
	{\em a}-Protein from {{\em Amphidinium carterae}}},
  journal = JPCA,
  year = {1999},
  volume = {103},
  pages = {2267--2273}
}

@ARTICLE{BELR99,
  author = {H. Belrhali and P. Nollert and A. Royant and C. Menzel and J. P.
	Rosenbusch and E. M. Landau and E. Pebay-Peyroula},
  title = {Protein, lipid and water organization in bacteriorhodopsin crystals:
	{A} molecular view of the purple membrane at 1.9 \AA\ resolution},
  journal = {Structure},
  year = {1999},
  volume = {7},
  pages = {909--917}
}

@ARTICLE{PEBA99,
  author = {H. Belrhali and P. Nollert and A. Royant and C. Menzel and J. P.
	Rosenbusch and E. M. Landau and E. Pebay-Peyroula},
  title = {Protein, lipid and water organization in bacteriorhodopsin crystals:
	a molecular view of the purple membrane at 1.9 \AA\ resolution},
  journal = {Structure},
  year = {1999},
  volume = {7},
  pages = {909--917}
}

@ARTICLE{BENN99A,
  author = {{Ben-Nun}, M and Mart{\'{\i}}nez, T J},
  title = {Exploiting Temporal Non-locality to Remove Scaling Bottlenecks in
	Non-adiabatic Quantum Dynamics},
  journal = {J. Chem. Phys.},
  year = {1999},
  volume = {110},
  pages = {4134--4140}
}

@ARTICLE{BENN99B,
  author = {{Ben-Nun}, M and Mart{\'{\i}}nez, T J},
  title = {Electronic Absorption and Resonance {Raman} Spectroscopy from {\it
	Ab Initio} Quantum Molecular Dynamics},
  journal = {J. Phys. Chem.},
  year = {1999},
  volume = {103},
  pages = {10517--10527}
}

@INPROCEEDINGS{BHAN99,
  author = {Milind Bhandarkar and Gila Budescu and William F. Humphrey and Jesus
	A. Izaguirre and Sergei Izrailev and Laxmikant V. Kal{\'e} and Dorina
	Kosztin and Ferenc Molnar and James C. Phillips and Klaus Schulten},
  title = {{BioCoRE}: {A} Collaboratory for Structural Biology},
  booktitle = {Proceedings of the {SCS} International Conference on Web-Based Modeling
	and Simulation},
  year = {1999},
  editor = {Agostino G. Bruzzone and Adelinde Uchrmacher and Ernest H. Page},
  pages = {242--251},
  address = {San Francisco, California},
  annote = {URL: http://cpsi4.dibe.unige.it/~websim; the paper has been assigned
	a code 5427.8638}
}

@ARTICLE{BIRG99,
  author = {R.~R.~Birge and N.~B.~Gillepsie and E.~W.~Izaguirre and A.~Kusnetow
	and A.~F.~Lawrence and D.~Singh and Q.~W.~Song and E.~Schmidt and
	J.~.A.~Stuart and S.~Seetharaman and K.~J.~Wise},
  title = {Biomolecular electronics: Protein-based associative processors and
	volumetric memories.},
  journal = JPC,
  year = {1999},
  volume = {103},
  pages = {10746--10766},
  number = {49}
}

@ARTICLE{BOAR99,
  author = {John Board and Klaus Schulten},
  title = {The Fast Multipole Algorithm},
  journal = IEEECSE,
  year = {1999},
  note = {In press.}
}

@CONFERENCE{BFRS99,
  author = {D. Bonachea and K. Fisher and A. Rogers and F. Smith},
  title = {Hancock: A Language for Processing Very Large-Scale Data},
  booktitle = {Proceedings of USENIX Second Conference on Domain-Specific Languages},
  year = {1999},
  publisher = {Austin, TX}
}

@ARTICLE{BoLL99,
  author = {Stephen~D. Bond and Benedict~J. Leimkuhler and Brian~B. Laird},
  title = {The {N}os\'e--{P}oincar\'e Method for Constant Temperature Molecular
	Dynamics},
  journal = {J. Comput.\ Phys},
  year = {1999},
  volume = {151},
  pages = {114--134},
  number = {1}
}

@ARTICLE{BOPP99,
  author = {M.A. Bopp and A. Sytnik and T.D. Howard and R.J. Cogdell and R.M.
	Hochstrasser},
  title = {The dynamics of structural deformations of immobilized single light-harvesting
	complexes},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1999},
  volume = {96},
  pages = {11271--11276}
}

@ARTICLE{BRAC99,
  author = {D. Bouzida and P. A. Rejto and S. Arthur and A. B. Colson and S.
	T. Freer and D. K. Gehlhaar and V. Larson and B. A. Luty and P. W.
	Rose and G. M. Verkhivker},
  title = {Computer simulation of ligand-protein binding with ensemble of protein
	conformations: A {M}onte {C}arlo study of {HIV}-1 protease binding
	energy landscapes},
  journal = IJQC,
  year = {1999},
  volume = {72},
  pages = {73--84}
}

@ARTICLE{VANB99B,
  author = {M.E. van Brederode and F. van Mourik and I.H.M. van Stokkum and M.R.
	Jones and R. van Grondelle},
  title = {Multiple pathways for ultrafast transduction of light energy in the
	photosynthetic reaction center of {\em {R}hodobacter sphaeroides}},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1999},
  volume = {96},
  pages = {2054--2059}
}

@ARTICLE{VANB99A,
  author = {M.E. van Brederode and I.H.M. van Stokkum and E. Katilius and F.
	van Mourik and M.R. Jones and R. van Grondelle},
  title = {Primary charge separation routes in the {B}{C}hl:{B}{P}he heterodimer
	reaction centers of {\em {R}hodobacter sphaeroides}},
  journal = {Biochem.},
  year = {1999},
  volume = {38},
  pages = {7545--7555}
}

@BOOK{BuMa99,
  title = {Efficient {C\texttt{++}}, Performance Programming Techniques},
  publisher = {Addison-Wesley},
  year = {1999},
  author = {D. Bulka and D. Mayhew}
}

@ARTICLE{CANT99,
  author = {Robert S. Cantor},
  title = {The influence of membrane lateral pressures on simple geometric models
	of protein conformational equilibria},
  journal = {{C}hemistry and {P}hysics of {L}ipids},
  year = {1999},
  volume = {101},
  pages = {45--56}
}

@ARTICLE{CANT99A,
  author = {Robert S. Cantor},
  title = {Lipid composition and the lateral pressure profile in bilayers},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {2625--2639}
}

@ARTICLE{CARB99,
  author = {D. Carbonera and G. Giacometti and U. Segre and E. Hofmann and R.
	G. Hiller},
  title = {Structure-Based Calculations of the Optical Spectra of the Light-Harvesting
	Peridinin-Chlorophyll-Protein Complexes from {{\em Amphidinium carterae}}
	and {{\em Heterocapsa pygmaea}}},
  journal = JPCB,
  year = {1999},
  volume = {103},
  pages = {6349--6356}
}

@ARTICLE{CaMM99,
  author = {Heather A. Carlson and Kevin M. Masukawa and J. Andrew McCammon},
  title = {Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided
	Drug Design},
  journal = JPCA,
  year = {1999},
  volume = {103},
  pages = {10213--10219},
  pdf = {Papers/CaMM99.pdf}
}

@ARTICLE{CARR99,
  author = {Mariano Carrion-Vazquez and Andres Oberhauser and Susan Fowler and
	Piotr Marszalek and Sheldon Broedel and Jane Clarke and Julio Fernandez},
  title = {Mechanical and chemical unfolding of a single protein: A comparison},
  journal = PNAS,
  year = {1999},
  volume = {96},
  pages = {3694--3699}
}

@ARTICLE{CASH99,
  author = {A.R. Cashmore and J.A Jarillo and Y-J.Wu and D. Liu},
  title = {Cryptochromes: Blue Light Receptors for Plants and Animals},
  journal = SCI,
  year = {1999},
  volume = {284},
  pages = {760--765}
}

@ARTICLE{CSSB99,
  author = {A. Cha and G.~E. Snyder and P.~R. Selvin and F. Bezanilla},
  title = {Atomic scale movements of the voltage sensor in a voltage-gated ion
	channel},
  journal = NAT,
  year = {1999},
  volume = {402},
  pages = {809--813}
}

@INPROCEEDINGS{CHRI99,
  author = {R.L. Christensen},
  title = {The electronic states of carotenoids},
  booktitle = {The photochemistry of carotenoids},
  year = {1999},
  editor = {H. Frank and A.J. Young and G. Britton and R.J. Cogdell},
  pages = {137--159},
  address = {The Netherlands},
  publisher = {Kluwer}
}

@ARTICLE{CAHK99,
  author = {S. Chung and T. W. Allen and M. Holes and S. Kuyucak},
  title = {Permeation of Ions Across the Potassium Channel: Brownian Dynamics
	Studies},
  journal = {Biophysical Journal},
  year = {1999},
  volume = {77},
  pages = {2517--2533}
}

@ARTICLE{COGD99,
  author = {R.J. Cogdell and N.W. Isaacs and T.D. Howard and K. McLuskey and
	N.J. Fraser and S.M. Prince},
  title = {How photosynthetic bacteria harvest solar energy},
  journal = {J.~Bacteriol.},
  year = {1999},
  volume = {181},
  pages = {3869--3879},
  annote = {Recent review on structures of LHs}
}

@ARTICLE{CoLZ99,
  author = {A.~Corradi and L.~Leonardi and F.~Zambonelli},
  title = {Diffusive Load Balancing Policies for Dynamic Applications},
  journal = IEEECC,
  year = {1999},
  volume = {7},
  number = {1}
}

@ARTICLE{DAMJ99,
  author = {Ana Damjanovi\'c and Thorsten Ritz and Klaus Schulten},
  title = {Energy Transfer Between Carotenoids and Bacteriochlorophylls in a
	Light Harvesting Protein},
  journal = PRE,
  year = {1999},
  volume = {59},
  pages = {3293--3311}
}

@ARTICLE{DaGM99,
  author = {Xavier Daura and Wilfred F. van Gunsteren and Alan E. Mark},
  title = {Folding-Unfolding Thermodynamics of a {B}-Heptapeptide From Equilibrium
	Simulations},
  journal = PRO,
  year = {1999},
  volume = {34},
  pages = {269--280},
  annote = {none}
}

@ARTICLE{DEUT99A,
  author = {M.E. Deutschlander and S.C. Borland and J.B. Phillips},
  title = {Extraocular magnetic compass in newts},
  journal = NAT,
  year = {1999},
  volume = {400},
  pages = {324--325}
}

@ARTICLE{DEUT99,
  author = {M.E. Deutschlander and J.N. Phillips and S.C. Borland},
  title = {The case for light-dependent magnetic orientation in animals},
  journal = {J.~Exp.~Biol.},
  year = {1999},
  volume = {202},
  pages = {891--908}
}

@ARTICLE{DiOt99,
  author = {R. Dillon and H. G. Othmer},
  title = {A mathematical model for outgrowth and spatial patterning of the
	vertebrate limb bud},
  journal = JTB,
  year = {1999},
  volume = {197},
  pages = {297--330},
  number = {3}
}

@ARTICLE{DMIT99,
  author = {Oleg Y. Dmitriev and Phil C. Jones and Robert H. Fillingame},
  title = {Structure of the subunit c oligomer in the F$_1$F$_0$ ATP synthase:
	Model derived from solution structure of the monomer and cross-linking
	in the native enzyme},
  journal = PNAS,
  year = {1999},
  volume = {96},
  pages = {7785--7790}
}

@ARTICLE{EDMA99,
  author = {K. Edman and P. Nollet and A. Royant and H. Belrhali and E. Pebay-Peyroula
	and J. Hajdu and R. Neutze and E. M. Landau},
  title = {High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin
	photocycle},
  journal = NAT,
  year = {1999},
  volume = {401},
  pages = {822--826}
}

@ARTICLE{ElMO99,
  author = {Ron Elber and Jaroslaw Meller and Roberto Olender},
  title = {Stochastic path approach to compute atomically detailed trajectories:
	Application to the folding of {C} peptide},
  journal = {Physical Chemistry B},
  year = {1999},
  volume = {103},
  pages = {899--911},
  number = {6}
}

@ARTICLE{ErNi99,
  author = {M. A. Eriksson and L. Nilsson},
  title = {Structural and dynamic differences of the estrogen receptor {D}{N}{A}-binding
	domain, binding as a dimer and as a monomer to {D}{N}{A}:molecular
	dynamics simulated studies},
  journal = {Eur Biophys J},
  year = {1999},
  volume = {28},
  pages = {102--111}
}

@ARTICLE{EVAN99,
  author = {Evan Evans and Ken Ritchie},
  title = {Strength of a Weak Bond Connecting Flexible Polymer Chains},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {2439--2447}
}

@ARTICLE{FeHB99,
  author = {K. Anton Feenstra and Berk Hess and Herman J.C. Berendsen},
  title = {Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations
	of Hydrogen-Rich Systems},
  journal = JCC,
  year = {1999},
  volume = {20},
  pages = {786--798},
  number = {8},
  nremark = {gives frequencies}
}

@ARTICLE{FEIG99,
  author = {M.~Feig and B.~M.~Pettitt.},
  title = {Modeling high resolution hydration patterns in correlation with {DNA}
	sequence and conformation},
  journal = JMB,
  year = {1999},
  volume = {286},
  pages = {1075--1095}
}

@ARTICLE{FELL99,
  author = {Scott E. Feller and Richard W. Pastor},
  title = {Constant surface tension simulations of lipid bilayers: The sensitivity
	of surface areas and compressibilities},
  journal = JCP,
  year = {1999},
  volume = {111},
  pages = {1281--1287},
  number = {3}
}

@ARTICLE{FORS99A,
  author = {Christian Forst and Klaus Schulten},
  title = {Phylogenetic Analysis of Metabolic Pathways},
  journal = {Journal of Molecular Evolution},
  year = {1999},
  note = {Submitted.}
}

@ARTICLE{FORS99B,
  author = {Christian Forst and Klaus Schulten},
  title = {Evolution of Metabolisms: {A} new Method for the Comparison of Metabolic
	Pathways using Genomics Information},
  journal = {Journal of Computational Biology},
  year = {1999},
  volume = {6},
  pages = {343--360}
}

@INPROCEEDINGS{FORS99,
  author = {Christian V. Forst and Klaus Schulten},
  title = {Evolution of Metabolisms: {A} New Method for the Comparison of Metabolic
	Pathways},
  booktitle = {Proceedings of the Third Annual International Conference on Computational
	Molecular Biology},
  year = {1999},
  editor = {Sorin Istrail and Pavel Pevzner and Michael Waterman},
  pages = {174--180},
  address = {Lyon, France},
  publisher = {ACM Press, New York}
}

@ARTICLE{FRAN99,
  author = {F. Francia and J. Wang and G. Venturoli and A. Melandri and W.P.
	Barz and D. Oesterhelt},
  title = {The reaction cnter-{LH1} antenna complex of {\em {R}hodobacter sphaeroides}
	contains one {PufX} molecule which is involved in dimerization of
	this complex},
  journal = {Biochem.},
  year = {1999},
  volume = {38},
  pages = {6834--6845}
}

@ARTICLE{FRIE99,
  author = {Friesner, R. A. and Murphy, R. B. and Beachy, M. D. and Ringnalda,
	M. N. and Pollard, W. T. and Dunietz, B. D. and Cao, Y. X.},
  title = {Correlated ab initio electronic structure calculations for large
	molecules},
  journal = JPC,
  year = {1999},
  volume = {103},
  pages = {1913},
  abstract = {We discuss computational methods for carrying out correlated ab initio
	electronic structure calculations for large systems. The focus is
	on two types of methods: density functional theory (DFT) and localized
	orbital methods such as local MP2 (LMP2) and a multireference version
	based upon a generalized valence bond reference wave function, GVB-LMP2.
	The computational performance of both approaches using pseudospectral
	numerical methods is documented, and calculated thermochemical and
	conformational energetics are compared to experimental data.}
}

@ARTICLE{GMM+99,
  author = {E. A. Gaffney and P. K. Maini and C. D. McCaig and M. Zhao and J.
	V. Forrester},
  title = {Modelling corneal epithelial wound closure in the presence of physiological
	electric fields via a moving boundary formalism},
  journal = {{IMA} J. OF Mathematics Applied in Medicine and Biology},
  year = {1999},
  volume = {16},
  pages = {369--393}
}

@ARTICLE{GALL99,
  author = {A. Gall and N.J. Fraser and M.-C. Bellissent-Funel and H. Scheer
	and B. Robert and R.J. Cogdell},
  title = {Bacteriochlorin-protein interactions in native B800-B850, B800 deficient
	and B800-Bchl$a_p$-reconstituted complexes from {\em {R}hodopseudomonas
	acidophila}, strain 10050},
  journal = {FEBS Lett.},
  year = {1999},
  volume = {449},
  pages = {269--272}
}

@ARTICLE{GALL99A,
  author = {A. Gall and B. Robert},
  title = {Characterization of the different peripheral light-harvesting complexes
	from high- and low-light grown cells from {\em {R}hodopseudomonas
	palustris}},
  journal = {Biochem.},
  year = {1999},
  volume = {38},
  pages = {5185--5190}
}

@ARTICLE{GeRB99,
  author = {J. Daniel Gezelter and Eran Rabani and B. J. Berne},
  title = {Calculating the hopping rate for diffusion in molecular liquids:
	CS$_{2}$},
  journal = {J. Chem.\ Phys.},
  year = {1999},
  volume = {110},
  pages = {3444}
}

@ARTICLE{GPP+99,
  author = {S. Gory-Faur\'e and M.-{\uppercase{H}} Prandini and H. Pointu and
	V. Roullot and I. Pignot-\uppercase{P}aintrand and M. Vernet and
	P. Huber},
  title = {Role of vascular endothelial-cadherin in vascular morphogenesis},
  journal = {Development},
  year = {1999},
  volume = {126},
  pages = {2093--2102},
  annote = {Vascular transmembrane interendothelial endothelial (VE)-cadherin
	is an adhesive transmembrane protein specifically expressed at junctions.
	Its extracellular domain exhibits Ca2+-dependent homophilic reactivity
	promoting cell-cell recognition. Mice deficient in VE-cadherin die
	at mid-gestation resulting from severe vascular defects. At the early
	phases of vascular development (E8.5) of VE-cadherin-deficient embryos
	in situ differentiation of endothelial cells was delayed although
	their differentiation program appeared normal. Vascularization was
	defective in the anterior part of the embryo while dorsal aortae
	and vitelline and umbilical arteries formed normally in the caudal
	part. At E9 25 organization of endothelial cells into large vessels
	was incomplete and angiogenesis was impaired in mutant embryos. Defects
	were more severe in extraembryonic vasculature. Blood islands of
	the yolk sac and clusters of angioblasts in allantois failed to establish
	a capillary plexus and remained isolated. This was not due to defective
	cell-cell recognition as endothelial cells formed intercellular junctions
	as shown by electron microscopy. These data indicate that VE-cadherin
	is dispensable for endothelial homophilic adhesion but is required
	for vascular morphogenesis. PY 1999},
  from = {INSTITUTE OF SCIENTIFIC INFORMATION:}
}

@ARTICLE{GrZu99,
  author = {M. Griebel and G. Zumbusch},
  title = {Parallel Multigrid in an Adaptive {PDE} Solver Based on Hashing and
	Space-Filled Curves},
  journal = JPCP,
  year = {1999},
  volume = {25},
  pages = {827--843},
  number = {7}
}

@BOOK{GrLT94,
  title = {Using {MPI}-2 - Advanced Features of the Message-Passing Interface},
  publisher = {{MIT} Press},
  year = {1999},
  author = {W. Gropp and E. Lusk and T. Thakur}
}

@ARTICLE{GULL99,
  author = {Justin Gullingsrud and Rosemary Braun and Klaus Schulten},
  title = {Reconstructing Potentials of Mean Force Through Time Series Analysis
	of Steered Molecular Dynamics Simulations},
  journal = JCMP,
  year = {1999},
  volume = {151},
  pages = {190--211},
  annote = {Special Issue on Computational Biophysics.}
}

@ARTICLE{GuBS99,
  author = {J. R. Gullingsrud and R. Braun and K. SchultenXS},
  title = {Reconstructing potentials of mean force through time series analysis
	of steered molecular dynamics simulations},
  journal = {J. Comput.\ Phys},
  year = {1999},
  volume = {151},
  pages = {190--211},
  number = {1}
}

@ARTICLE{HaCr99,
  author = {Scott Haney and James Crotinger},
  title = {How templates enable high-performance scientific computing in {C}\texttt{++}},
  journal = {Computing In Science \& Engineering},
  year = {1999},
  volume = {1},
  pages = {66--72},
  number = {4},
  note = {POOMA reference}
}

@ARTICLE{HaOS99,
  author = {D.~J. Hardy and D.~I. Okunbor and R.~D. Skeel},
  title = {Symplectic Variable Stepsize Integration for {$N$}-Body Problems},
  journal = {Appl.\ Numer.\ Math.},
  year = {1999},
  volume = {29},
  pages = {19--30},
  nack = {Work by first and second authors supported in part by NSF Grant CCR-9408973;
	work by first and third authors supported in part by NSF Grant DMS-9600088,
	NSF Grant BIR-9318159, and NIH Grant P41RR05969.},
  nremark = {Available by anonymous ftp from ftp.cs.uiuc.edu as /pub/faculty/skeel/Preprints/HaOS9y.ps,
	PDF at http://www.elsevier.nl/locate/apnum}
}

@BOOK{HARO99,
  title = {XML Bible},
  publisher = {IDG Books Worldwide},
  year = {1999},
  author = {E.~R.~Harold},
  address = {Foster City}
}

@ARTICLE{HEGI99,
  author = {Lise Heginbotham and Meredith LeMasurier and Ludmilla Kolmakova-Partensky
	and Christopher Miller},
  title = {Single {\em Streptomyces lividans} {K$^+$} channels: functional asymmetries
	and sidedness of proton activation},
  journal = JGP,
  year = {1999},
  volume = {114},
  pages = {551--559},
  annote = {channel activity is observed only when the intracellular side is
	at (physiologically unrealistically) low pH}
}

@ARTICLE{HePa99,
  author = {T. Hermann and D.~J. Patel},
  title = {Stitching Together RNA Tertiary Architectures},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {294},
  pages = {829--849}
}

@ARTICLE{HuMc99,
  author = {G. A. Huber and J. A. McCammon},
  title = {{OOMPAA}---{O}bject-oriented model for probing assemblages of atoms},
  journal = {J. Comput.\ Phys},
  year = {1999},
  volume = {151},
  pages = {264--282},
  number = {1}
}

@ARTICLE{HBRS99,
  author = {W. Huisinga and Ch. Best and R. Roitzsch and and Ch. Sch{\"u}tte
	and F. Cordes},
  title = {From Simulation Data to Conformational Ensembles: Structure and Dynamics
	based Methods},
  journal = JCC,
  year = {1999},
  volume = {20},
  pages = {1760--1774}
}

@ARTICLE{HoLi99,
  author = {V. H{\"o}sel and V. Liebscher},
  title = {Some thoughts on the modeling of biofilms},
  journal = {Mathematics and Statistics},
  year = {1999},
  note = {Available via http://ibb.gsf.de/preprints/1999/pp99-27.ps
	
	}
}

@MISC{IBM99,
  author = {IBM},
  title = {Python 101},
  year = {1999},
  note = {\url{http://www-128.ibm.com/developerworks/linux/library/l-python101.html}}
}

@PHDTHESIS{Izag99,
  author = {J.~A. Izaguirre},
  title = {Longer Time Steps for Molecular Dynamics},
  school = {University of Illinois at Urbana-Champaign},
  year = {1999},
  address = {Urbana, Illinois, USA},
  annote = {Also UIUC Technical Report UIUCDCS-R-99-2107. Available online via
	\texttt{http://www.cs.uiuc.edu/research/tech-reports.html}}
}

@PHDTHESIS{Izag99b,
  author = {J.~A. Izaguirre},
  title = {Longer Time Steps for Molecular Dynamics},
  school = {University of Illinois at Urbana-Champaign},
  year = {1999},
  note = {Also UIUC Technical Report UIUCDCS-R-99-2107. Available online via
	\texttt{http://www.cs.uiuc.edu/research/tech-reports.html}}
}

@ARTICLE{IzRS99,
  author = {J.~A. Izaguirre and S. Reich and R.~D. Skeel},
  title = {Longer Time Steps for Molecular Dynamics},
  journal = JCP,
  year = {1999},
  volume = {110},
  pages = {9853--9864},
  number = {19},
  nack = {nih97, gcag93, nsf96},
  nremark = {Available by anonymous ftp from ftp.cs.uiuc.edu as /pub/faculty/skeel/Preprints/IzRS9y.ps}
}

@ARTICLE{IZRA99,
  author = {Sergei Izrailev and Antony R. Crofts and Edward A. Berry and Klaus
	Schulten},
  title = {Steered Molecular Dynamics Simulation of the {Rieske} Subunit Motion
	in the Cytochrome~$bc_1$ Complex},
  journal = BJ,
  year = {1999},
  volume = {77},
  pages = {1753--1768}
}

@ARTICLE{JIAN99,
  author = {Y. Jiang and P. Swart and A. Saxena and M. Asipauskas and J. A. Glazier},
  title = {Hysteresis and Avalanches in Two-Dimensional Foam Rheology Simulations},
  journal = PRE,
  year = {1999},
  volume = {59},
  pages = {5819--5832},
  number = {5}
}

@BOOK{Josu99,
  title = {The {C\texttt{++}} Standard Library - A Tutorial and Reference},
  publisher = {Addison Wesley},
  year = {1999},
  author = {N.~M. Josuttis}
}

@ARTICLE{JUNG99,
  author = {C. Jungas and J.L. Ranck and J.L. Rigaud and P. Joliot and A. Vermeglio},
  title = {Supramolecular organization of the photosynthetic apparatus of {\em
	Rhodobacter sphaeroides}},
  journal = EMBO,
  year = {1999},
  volume = {18},
  pages = {534--542},
  number = {3}
}

@ARTICLE{KAKI99,
  author = {T. Kakitani and A. Kimura and H. Sumi},
  title = {Theory of excitation transfer in the intermediate coupling case},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {3720--3726}
}

@ARTICLE{Kale99,
  author = {Laxmikant Kal{\'e} and Robert Skeel and Milind Bhandarkar and Robert
	Brunner and Attila Gursoy and Neal Krawetz and James Phillips and
	Aritomo Shinozaki and Krishnan Varadarajan and Klaus Schulten},
  title = {{NAMD2: G}reater Scalability for Parallel Molecular Dynamics},
  journal = JCMP,
  year = {1999},
  volume = {151},
  pages = {283--312}
}

@ARTICLE{KaMO99,
  author = {C.\ Kane and J.\ E.\ Marsden and M.\ Ortiz},
  title = {Symplectic energy-momentum integrators},
  journal = {J. Math. Phys.},
  year = {1999},
  volume = {40},
  pages = {3353--3371}
}

@ARTICLE{KANZ99,
  author = {Makoto Kanzaki and Masahiro Magasawa and Itaru Kojima and Chikara
	Sato and Keiji Naruse and Masahiro Sokabe and Hidetoshi Iida},
  title = {Molecular identification of a eukaryotic, stretch-activated nonselective
	cation channel},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {882--886}
}

@ARTICLE{KAUF99,
  author = {David Kaufman and Ioan Kosztin and Klaus Schulten},
  title = {Expansion Method for Stationary States of Quantum Billiards},
  journal = AJP,
  year = {1999},
  volume = {67},
  pages = {133--141}
}

@ARTICLE{KaMi99,
  author = {M. Kawata and M. Mikami},
  title = {Acceleration of the canonical molecular dynamics simulation by the
	particle mesh {E}wald method combined with the multiple time-step
	integrator algorithm},
  journal = {Chemical Physics Letters},
  year = {1999},
  volume = {313},
  pages = {261--266},
  number = {1-2},
  annote = {The canonical molecular dynamics MD simulation was accelerated by
	the integrated method of the multiple time-step . integrator algorithm
	combined with the particle mesh Ewald method PMEM applied not only
	to the calculation of the Coulomb interaction but also of the Van
	der Waals interaction. Although the previous integrated method, in
	which the PMEM was used in the calculation only for the Coulomb interaction,
	yielded a significant acceleration of the MD simulation, a further
	acceleration by a factor of about 2 in the entire MD simulation was
	obtained by extension of the integrated method to the Van der Waals
	interaction.}
}

@ARTICLE{KaHM99,
  author = {Y. N. Kaznessis and D. A. Hill and E. J. Maginn},
  title = {Molecular dynamics simulations of dielectric relaxation of concentrated
	polymer solutions},
  journal = {J. Chem.\ Phys.},
  year = {1999},
  volume = {111},
  pages = {1325--1334}
}

@ARTICLE{KeMi99,
  author = {C.~E.~Kee and C.~T.~Miller},
  title = {C\texttt{++} Implementations of Numerical Methods for Solving Differential-Algebraic
	Equations: Design and Optimization Considerations},
  journal = ACMTMS,
  year = {1999},
  pages = {377--403},
  number = {4},
  key = {25}
}

@ARTICLE{KIKU99,
  author = {J. Kikuchi and T. Asakura and P.A. Loach and P.S. Parkes-Loach and
	K. Shimada and C. N. Hunter and M.J. Conroy and M.P. Williamson},
  title = {A light-harvesting antenna protein retains its folded conformation
	in the absence of protein-lipid and protein-pigment interactions},
  journal = {Biopolymers},
  year = {1999},
  volume = {49},
  pages = {361--372}
}

@ARTICLE{KLEI99A,
  author = {F.J. Kleima and S. Hobe and F. Calkoen and M.L. Urbanus and E.J.G.
	Peterman and R. {van Grondelle} and H. Paulsen and H. {van Amerongen}},
  title = {Decreasing the chlorophyll $a/b$ ration in reconstituted {LHCII}:
	structural and functional consequences},
  journal = {Biochem.},
  year = {1999},
  volume = {38},
  pages = {6587--6596}
}

@ARTICLE{KoLe99,
  author = {P. Koehl and M. Levitt},
  title = {A Brighter Future for Protein Structure Prediction},
  journal = {Nature Struct. Biol.},
  year = {1999},
  volume = {6},
  pages = {108--111}
}

@ARTICLE{KOSZ99A,
  author = {Dorina Kosztin and Richard Gumport and Klaus Schulten},
  title = {Probing the role of structural water in a duplex oligodeoxyribonucleotide
	containing a water-mimicking base analogue},
  journal = NAR,
  year = {1999},
  volume = {27},
  pages = {3550--3556},
  number = {17}
}

@ARTICLE{KOSZ99,
  author = {Dorina Kosztin and Sergei Izrailev and Klaus Schulten},
  title = {Unbinding of Retinoic Acid from its Receptor Studied by Steered Molecular
	Dynamics},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {188--197}
}

@ARTICLE{KRAM99,
  author = {Andr{\'e} Krammer and Hui Lu and Barry Isralewitz and Klaus Schulten
	and Viola Vogel},
  title = {Forced Unfolding of the Fibronectin Type {III} Module Reveals a Tensile
	Molecular Recognition Switch},
  journal = PNAS,
  year = {1999},
  volume = {96},
  pages = {1351--1356}
}

@ARTICLE{KRUE99,
  author = {B.P. Krueger and G.D. Scholes and I.R. Gould and G.R. Fleming},
  title = {Carotenoid mediated {B}800-{B}850 coupling in {LH}2},
  journal = {Phys.~Chem.~Comm.},
  year = {1999},
  volume = {8},
  pages = {9/03172C}
}

@ARTICLE{KRUE99A,
  author = {B.P. Krueger and J. Yom and P.J. Walla and G.R. Fleming},
  title = {Observation of the {S}$_1$ state of spheroidene in {LH}2 by two-photon
	fluorescence excitation},
  journal = {Chem.~Phys.~Lett.},
  year = {1999},
  volume = {310},
  pages = {57--64}
}

@ARTICLE{LAPO99,
  author = {K. Lapouge and A. N{\"a}veke and A. Gall and A. Ivancich and J. Seguin
	and H. Scheer and J.N. Sturgis and T.A. Mattioli and B. Robert},
  title = {Conformation of bacteriochlorophyll molecules in photosynthetic proteins
	from purple bacteria},
  journal = {Biochem.},
  year = {1999},
  volume = {38},
  pages = {11115--11121}
}

@INCOLLECTION{LU99B,
  author = {Hui Lu and Andr{\'e} Krammer and Barry Isralewitz and Viola Vogel
	and Klaus Schulten},
  title = {Computer modeling of force-induced titin domain unfolding},
  booktitle = {Elastic Filaments of the Cell},
  publisher = {Kluwer Academic/Plenum Publishers},
  year = {1999},
  editor = {Jerry Pollack and Henk Granzier},
  chapter = {1},
  address = {New York, NY},
  note = {In press.}
}

@ARTICLE{LU99,
  author = {Hui Lu and Klaus Schulten},
  title = {Steered Molecular Dynamics Simulations of Force-induced Protein Domain
	Unfolding},
  journal = PRO,
  year = {1999},
  volume = {35},
  pages = {453--463}
}

@ARTICLE{LU99A,
  author = {Hui Lu and Klaus Schulten},
  title = {Steered Molecular Dynamics Simulation of Conformational Changes of
	Immunoglobulin Domain {I27} Interpret Atomic Force Microscopy Observations},
  journal = CP,
  year = {1999},
  volume = {247},
  pages = {141--153}
}

@ARTICLE{LU99C,
  author = {Hui Lu and Klaus Schulten},
  title = {The Key Event in Force-Induced Unfolding of Titin's Immunoglobulin
	Domains},
  journal = BJ,
  year = {1999},
  note = {Submitted.}
}

@ARTICLE{LUEC99,
  author = {H. L{\"u}cke and B. Schobert and H. T. Richter and J. P. Cartailler
	and J. K. Lanyi},
  title = {Structure of Bacteriorhodopsin at 1.55 \AA\ Resolution},
  journal = JMB,
  year = {1999},
  volume = {291},
  pages = {899--911}
}

@ARTICLE{LUEC99a,
  author = {H. L{\"u}cke and B. Schobert and H. T. Richter and J. P. Cartailler
	and J. K. Lanyi},
  title = {Structure Changes in Bacteriorhodopsin During Ion Transport at 2
	\AA\ Resolution},
  journal = SCI,
  year = {1999},
  volume = {286},
  pages = {255--260}
}

@ARTICLE{MaMa99,
  author = {Michael D. Macedonia and Edward J. Maginn},
  title = {A biased grand canonical {M}onte {C}arlo method for simulating adsorption
	using all-atom and branched united atom models},
  journal = {Mol. Phys.},
  year = {1999},
  volume = {96},
  pages = {1375--1390},
  number = {9}
}

@ARTICLE{MAIN99,
  author = {Fran{\c c}ois Maingret and Michel Fosset and Florian Lesage and Michel
	Mazdunski and Eric Honor{\'e}},
  title = {{TRAAK} is a mammalian neuronal mechano-gated {K$^+$} channel},
  journal = JBC,
  year = {1999},
  volume = {274},
  pages = {1381--1387},
  number = {3}
}

@ARTICLE{MaDe99,
  author = {Vasilios I. Manousiouthakis and Michael W. Deem},
  title = {Strict detailed balance is unnecessary in {M}onte {C}arlo simulation},
  journal = JCP,
  year = {1999},
  volume = {110},
  pages = {2753--2756},
  number = {6}
}

@ARTICLE{MaPH99,
  author = {A.~F. M. Mar\'ee and A.~V. Panfilov and P.~Hogeweg},
  title = {Migration and thermotaxis of {\em {D}ictyostelium discoideum} slugs,
	a model study},
  journal = {J. Theor. Biol.},
  year = {1999},
  volume = {199},
  pages = {297--309},
  number = {3}
}

@ARTICLE{MaPH99a,
  author = {A.~F. M. Mar\'ee and A.~V. Panfilov and P.~Hogeweg},
  title = {Phototaxis during the slug stage of {D}ictyostelium discoideum: a
	model study},
  journal = {Proc. Roy. Soc. of London Series B - Biological Sciences},
  year = {1999},
  volume = {266},
  pages = {1351--1360},
  number = {1426}
}

@ARTICLE{MARS99,
  author = {Piotr E. Marszalek and Hui Lu and Hongbin Li and Mariano Carrion-Vazquez
	and Andres F. Oberhauser and Klaus Schulten and Julio M. Fernandez},
  title = {Mechanical unfolding intermediates in titin modules},
  journal = NAT,
  year = {1999},
  volume = {402},
  pages = {100--103}
}

@ARTICLE{MAY99,
  author = {Sylvio May and Avinoam Ben-Shaul},
  title = {Molecular Theory of lipid-protein interaction and the \mbox{$L_\alpha-H_{||}$}
	transition},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {751--767}
}

@ARTICLE{MEHT99,
  author = {Amid D. Mehta and Matthias Rief and James A. Spudich and David A.
	Smith and Robert M. Simmons},
  title = {Single Molecule Biomechanics with Optical Methods},
  journal = SCI,
  year = {1999},
  volume = {283},
  pages = {1689--1695}
}

@ARTICLE{MERC99,
  author = {Ian P. Mercer and Ian R. Gould and David R. Klug},
  title = {A Quantum Mechanical/Molecular Mechanical Approach to Relaxation
	Dynamics: Calculation of the Optical Properties of Solvated Bacteriochlorophyll-a},
  journal = JPCB,
  year = {1999},
  volume = {103},
  pages = {7720--7727}
}

@INPROCEEDINGS{MOFF99,
  author = {K. Moffat and {J.-P.} Changeux and D. M. Crothers and H. Grubmueller
	and G. U. Nienhaus and M. U. Palma and F. G. Parak and K. Schulten
	and A. Warshel},
  title = {Group Report: {How} Does Complexity Lead to an Apparently Simple
	Function?},
  booktitle = {Simplicity and Complexity in Proteins and Nucleic Acids},
  year = {1999},
  editor = {H. Frauenfelder and J. Deisenhofer and P. G. Wolynes},
  address = {Berlin},
  publisher = {Dahlem University Press},
  note = {In press.},
  annote = {Berlin, May 17-22, 1998}
}

@ARTICLE{MOLN99A,
  author = {Ferenc Molnar and Michal Ben-Nun and Todd J. {Mart{\'{\i}}nez} and
	Klaus Schulten},
  title = {Characterization of a Conical Intersection between the Ground and
	First Excited State for a Retinal Analog},
  journal = {Journal of Molecular Structure (THEOCHEM)},
  year = {1999},
  volume = {a special WATOC issue},
  note = {In press.}
}

@ARTICLE{MOLN99,
  author = {Ferenc Molnar and Lawrence S. Norris and Klaus Schulten},
  title = {Simulated Unbinding and Binding of Fatty Acid Substrates in the Cyclooxygenase
	Site of Prostaglandin {H$_{2}$} Synthase-1},
  journal = BJ,
  year = {1999},
  note = {Submitted.}
}

@ARTICLE{MUKA99,
  author = {K. Mukai and S. Abe and H. Sumi},
  title = {Theory of rapid excitation-energy transfer from B800 to optically-forbidden
	exciton states of B850 in the antenna system LH2 of Photosynthetic
	purple bacteria},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {6096--6102}
}

@ARTICLE{NAGA99,
  author = {V. Nagarajan and E.T. Johnson and J.C. Williams and W.W. Parson},
  title = {Femtosecond pump-sprobe spectroscopy of the B850 antenna complex
	of {\em {R}hodobacter sphaeroides} at room temperature},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {2297--2309}
}

@INBOOK{NaWa99,
  chapter = {21},
  pages = {859--898},
  title = {Molecular Dynamics. From Classical to Quantum Methods},
  publisher = {Elsevier Science B.V.},
  year = {1999},
  author = {Frederico Nardi and Rebecca Wade},
  edition = {First}
}

@BOOK{NeBa99,
  title = {{M}onte {C}arlo methods in statistical physics},
  publisher = {Oxford University Press, Oxford},
  year = {1999},
  author = {M.~E. J. Newman and G.~T. Barkema}
}

@ARTICLE{VANO99,
  author = {A.M. van Oijen and M. Ketelaars and J. K\"{o}hler and T.J. Aartsma
	and J. Schmidt},
  title = {Unraveling the electronic structure of individual photosynthetuc
	pigment-protein complexes},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {400--402}
}

@ARTICLE{ONAK99,
  author = {K. Onaka and R. Fujii and H. Nagae and M. Kuki and Y. Koyama and
	Y. Watanabe},
  title = {The state energy and the displacements of the potential minima of
	the 2A$_g^-$ state in all-{\em trans}-$\beta$-carotene as determined
	by fluorescence spectroscopy},
  journal = {Chem.~Phys.~Lett.},
  year = {1999},
  volume = {1--2},
  pages = {75--81}
}

@ARTICLE{PACI99,
  author = {Emanuele Paci and Martin Karplus},
  title = {Forced Unfolding of Fibronectin Type 3 Modules: An Analysis by Biased
	Molecular Dynamics Simulations},
  journal = JMB,
  year = {1999},
  volume = {288},
  pages = {441--459}
}

@ARTICLE{PWYO99,
  author = {A.G. Pavlovsky and M.G. Williams and Ye Qi-Zhuang and D.F. Ortwine
	and C. Purchase and A.D. White and V. Dhanaraj and B.D. Roth and
	L.L. Johnson and D. Hupe and C. Humblet and T.L. Blundell},
  title = {X-Ray Structure of Human Stromelysin Catalytic Domain Complexed With
	Non-peptide Inhibitors: Implications For Inhibitor Selectivity},
  journal = {Protein Science},
  year = {1999},
  volume = {8},
  pages = {1455--1462}
}

@ARTICLE{PeCC99,
  author = {E. Perozo and D. M. Cortes and L. G. Cuello},
  title = {Structural Rearrangements Underlying ${K}^+$ Channel Activation Gating},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {73--78}
}

@ARTICLE{PERO99,
  author = {Eduardo Perozo and D. Marien Cortes and Luis G. Cuello},
  title = {Structural rearrangements underlying {K}$^+$-channel activation gating},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {73--78}
}

@ARTICLE{Pfei99,
  author = {Ralf l. Pfeiffer},
  title = {XML Tutorials for Programmers},
  journal = {http://www.oasis-open.org/cover/xmlIntro.html},
  year = {1999},
  organization = {IBM XML Technology Group}
}

@ARTICLE{PHAN99,
  author = {A.~P.~Phan and J.~L.~Leroy and M.~Gueron.},
  title = {Determination of the residence time of water molecules hydrating
	{B'-DNA} and {B-DNA}, by zero-enhancement nuclear overhauser effect
	spectroscopy},
  journal = JMB,
  year = {1999},
  volume = {286},
  pages = {505--519}
}

@INPROCEEDINGS{PhWM99,
  author = {John B. Phillips and Wolfgang Wiltschko and Ursula Munro},
  title = {Visual system involvement in magnetoreception in birds},
  booktitle = {Proceedings 22 {I}nt. {O}rnithol. {C}ongress},
  year = {1999},
  editor = {N. Adams and R. Slotow},
  address = {Durban},
  publisher = {University of Natal}
}

@ARTICLE{PIEP99,
  author = {J. Pieper and J. Voigt and G.J. Small},
  title = {Chlorophyll $a$ {F}ranck-{C}ondon factors and excitation energy transfer},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {2319--2322}
}

@ARTICLE{POLI99,
  author = {T. Polivka and J.L. Herek and D. Zigmantas and H.-E. Akerlund and
	V. Sundstr{\"o}m},
  title = {Direct observation of the (forbidden) {S}$_1$ state in carotenoids},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1999},
  volume = {96},
  pages = {4914--4917}
}

@ARTICLE{PLBO99,
  author = {W. Porod and C. S. Lent and G. H. Berstein and A. O. Orlov and I.
	Amlani and G. L. Snider and J. L. Merz},
  title = {Quantum-Dot Cellular Automata: Computing with Coupled Quantum Dots},
  journal = {International Journal of Electronics},
  year = {1999},
  volume = {86},
  pages = {549 -- 590}
}

@ARTICLE{PKCM99,
  author = {M.\ J.\ Potter and P.\ D.\ Kirchhoff and H.\ A.\ Carlson and J.~A.\
	McCammon},
  title = {Molecular Dynamics of Cryptophane and its Complexes with Tetramethylammonium
	and Neopentane Using a Continuum Solvent Model},
  journal = JCC,
  year = {1999},
  volume = {20},
  pages = {956--970}
}

@ARTICLE{PRIN99,
  author = {Jan F. Prins and Jan Hermans and Geoffery Mann and Lars S. Nyland
	and Martin Simons},
  title = {A virtual environment for steered molecular dynamics},
  journal = {Future Generation Computer Systems},
  year = {1999},
  volume = {15},
  pages = {485--495}
}

@MISC{RAJ99,
  author = {Gopalan Suresh Raj},
  title = {The Factory Method (Creational) Design Pattern},
  howpublished = { http://gsraj.tripod.com/design/creational/factory/factory.html.},
  year = {1999}
}

@ARTICLE{RAND99,
  author = {Holly S. Randa and Lucy R. Forrest and Gregory A. Voth and Mark S.
	P. Sansom},
  title = {Molecular dynamics of synthetic leucine-serine ion channels in a
	phospholipid membrane},
  journal = BJ,
  year = {1999},
  volume = {77},
  pages = {2400--2410},
  number = {5}
}

@ARTICLE{SHEE99,
  author = {Drazen Raucher and Michael P. Sheetz},
  title = {Characteristics of a membrane reservoir buffering membrane tension},
  journal = BJ,
  year = {1999},
  volume = {77},
  pages = {1992--2002}
}

@ARTICLE{RAY99,
  author = {J. Ray and N. Makri},
  title = {Short-Range Coherence in the Energy Transfer of Photosynthetic Light-Harvesting
	Systems},
  journal = {J.~Phys.~Chem.~A},
  year = {1999},
  volume = {103},
  pages = {9417--9422}
}

@ARTICLE{Reic99,
  author = {S. Reich},
  title = {Backward Error Analysis for Numerical Integrators},
  journal = SJNA,
  year = {1999},
  volume = {36},
  pages = {1549--1570},
  nremark = {institution = Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin;
	month = July; the SC-96-21 version is outdated and not even close
	to the paper that i finally submitted, includes the symplectic variable
	step-size approach; it presents BEA in a very clean and neat way.
	I also inlcuded a discussion on the computation of time averages.}
}

@ARTICLE{RIEF99,
  author = {M. Rief and J. Pascual and M. Saraste and H. Gaub},
  title = {Single molecule force spectroscopy of spectrin repeats: Low unfolding
	forces in helix bundles},
  journal = JMB,
  year = {1999},
  volume = {286},
  pages = {553--561}
}

@ARTICLE{RoDe99,
  author = {C. J. Roberts and Pablo G. Debenedetti},
  title = {Structure and Dynamics in Concentrated, Amorphous Carbohydrate--Water
	Systems by Molecular Dynamics Simulation},
  journal = {J.\ Phys.\ Chem. B},
  year = {1999},
  volume = {103},
  pages = {7308--7318}
}

@ARTICLE{ROHS99,
  author = {Remo Rohs and Catherine Etchebest and Richard Lavery},
  title = {Unraveling Proteins: A Molecular Mechanics Study},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {2760--2768}
}

@ARTICLE{ROOS99,
  author = {B.~O.~Roos},
  title = {{Theoretical Studies of Electronically Excited States of Molecular
	Systems Using Multiconfigurational Perturbation Theory}},
  journal = ACR,
  year = {1999},
  volume = {32},
  pages = {137--144}
}

@ARTICLE{ROUX99,
  author = {Benoit Roux and Roderick MacKinnon},
  title = {The cavity and pore helices in the {KcsA} {K$^+$} channel: electrostatic
	stabilization of monovalent cations},
  journal = SCI,
  year = {1999},
  volume = {285},
  pages = {100--102}
}

@ARTICLE{SaDa99,
  author = {C.~Sagui and T.~A. Darden},
  title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic
	Effects},
  journal = ARBBS,
  year = {1999},
  volume = {28},
  pages = {155--179}
}

@ARTICLE{SXHL99,
  author = {R. Samudrala and Y. Xia and E. Huang and M. Levitt},
  title = {Ab initio Protein Structure Prediction Using a Combined Hierarchical
	Approach},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1999},
  volume = {S3},
  pages = {194--198}
}

@ARTICLE{SaSc99,
  author = {A. Sandu and T. Schlick},
  title = {Masking resonance artifacts in force-splitting methods for biomolecular
	simulations by extrapolative {L}angevin dynamics},
  journal = {J. Comput.\ Phys},
  year = {1999},
  volume = {151},
  pages = {74--113},
  number = {1}
}

@ARTICLE{SNKK99,
  author = {T. Sashima and H. Nagae and M. Kuki and Y. Koyama},
  title = {A new singlet-excited state of all-{\em trans}-spheroidene as detected
	by resonance-{R}aman excitation profiles},
  journal = {Chem.~Phys.~Lett.},
  year = {1999},
  volume = {299},
  pages = {187--194}
}

@ARTICLE{SCHL99,
  author = {Tamar Schlick and Robert Skeel and Axel Br{\"u}nger and Laxmikant
	Kal{\'e} and John A. {Board Jr.} and Jan Hermans and Klaus Schulten},
  title = {Algorithmic Challenges in Computational Molecular Biophysics},
  journal = JCMP,
  year = {1999},
  volume = {151},
  pages = {9--48},
  annote = {Special Issue on Computational Biophysics}
}

@ARTICLE{SSBK99,
  author = {Tamar Schlick and R.~D. Skeel and Axel T. Br{\"u}nger and Laxmikant
	V. Kal{\'e} and John A. {Board, Jr.} and Jan Hermans and Klaus Schulten},
  title = {Algorithmic Challenges in Computational Molecular Biophysics},
  journal = {J. Comput.\ Phys.},
  year = {1999},
  volume = {151},
  pages = {9--48},
  number = {1},
  nack = {NSF93},
  nremark = {Special issue}
}

@ARTICLE{SCHO99,
  author = {G.D. Scholes and I.R. Gould and R.J. Cogdell and G.R. Fleming},
  title = {{\em Ab initio} molecular orbital calculations of electronic couplings
	in the LH2 Bacterial light-harvesting complex of {\em {R}ps.~acidophila}},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {2543--2553}
}

@ARTICLE{ScWW99,
  author = {H. Schwichtenberg and G. Winter and H. Wallmeier},
  title = {Acceleration of molecular mechanic simulation by parallelization
	and fast multipole techniques},
  journal = {Parallel Computing},
  year = {1999},
  volume = {25},
  pages = {535--546}
}

@ARTICLE{SFHD99,
  author = {C. Sch{\"u}tte and A. Fischer and W. Huisinga and P. Deuflhard},
  title = {A Direct Approach to Conformational Dynamics Based on Hybrid {M}onte
	{C}arlo},
  journal = {J. Comput.\ Phys},
  year = {1999},
  volume = {151},
  pages = {146--168},
  number = {1}
}

@CONFERENCE{SiBe99,
  author = {E.~G. Sirer and B.~N. Bershad},
  title = {Using production grammars in software testing},
  booktitle = {Second conference on Domain Specific Languages},
  year = {1999},
  pages = {1183},
  publisher = {Society of Magnetic Resonance in Medicine, Inc.}
}

@ARTICLE{Skee99a,
  author = {R.~D. Skeel},
  title = {Symplectic Integration with Floating-Point Arithmetic and Other Approximations},
  journal = {Appl.\ Numer.\ Math.},
  year = {1999},
  volume = {29},
  pages = {3--18},
  nack = {NSF Grant DMS-9600088, NSF Grant BIR-9318159, and NIH Grant P41RR05969.},
  nremark = {Available by anonymous ftp from ftp.cs.uiuc.edu as /pub/faculty/skeel/Preprints/Skee9y.ps,
	PDF at http://www.elsevier.nl/locate/apnum}
}

@INCOLLECTION{Skee99b,
  author = {Robert D.~Skeel},
  title = {Integration Schemes for Molecular Dynamics and Related Applications},
  booktitle = {The Graduate Student's Guide to Numerical Analysis},
  publisher = {Springer-Verlag},
  year = {1999},
  editor = {M.~Ainsworth and J.~Levesley and M.~Marletta},
  volume = {26},
  series = {Springer Ser. Comput. Math.},
  pages = {119--176},
  address = {Berlin},
  nack = {This work was supported in part by NSF Grant DMS-9600088, NSF Grant
	BIR-9318159, and NIH Grant P41RR05969.}
}

@MISC{Lucr99,
  author = {G.~D. Smith and C. Ayyagari and D. Bedrov},
  title = {Lucretius: {A} molecular dynamics simulation program},
  year = {1999},
  note = { \texttt{\small http://www.che.utah.edu/\~{}gdsmith/mdcode/main.html}}
}

@ARTICLE{SOCC99,
  author = {N. Socci and J. Onuchic and P. Wolynes},
  title = {Stretching lattice models of protein folding},
  journal = PNAS,
  year = {1999},
  volume = {96},
  pages = {2031--2035}
}

@ARTICLE{SPEN99,
  author = {Robert H. Spencer and Geoffrey Chang and Douglas C. Rees},
  title = {'Feeling the pressure': structural insights into a gated mechanosensitive
	channel},
  journal = COSB,
  year = {1999},
  volume = {9},
  pages = {448--454}
}

@ARTICLE{Sto+99,
  author = {E. Stott and N.F. Britton and J.A. Glazier and M. Zajac},
  title = {Stochastic simulation of benign avascular tumor growth using the
	{P}otts model},
  journal = {Math. and Comp. Mod.},
  year = {1999},
  volume = {30},
  pages = {183--198}
}

@ARTICLE{SuOk99,
  author = {Yuji Sugita and Yuko Okamoto},
  title = {Replica-exchange molecular dynamics method for protein folding},
  journal = CPL,
  year = {1999},
  volume = {314},
  pages = {141--151}
}

@ARTICLE{SUKH99,
  author = {Sergei I. Sukharev and Wade J. Sigurdson and Ching Kung and Frederick
	Sachs},
  title = {Energetics and spatial parameters for gating of the bacterial large
	conductance mechanosensitive channel, {MscL}},
  journal = JGP,
  year = {1999},
  volume = {113},
  pages = {525--539}
}

@ARTICLE{SUMI99,
  author = {H. Sumi},
  title = {Theory on rates of excitation-energy transfer between molecular aggregates
	through distributed transition dipoles with application to the antenna
	system in bacterial photosynthesis},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {252--260}
}

@ARTICLE{SUND99,
  author = {V. Sundstrom and T. Pullerits and R. van Grondelle},
  title = {Photosynthetic light-harvesting: Reconciling dynamics and structure
	of purple bacterial LH2 reveals function of photosynthetic unit},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {2327--2346}
}

@ARTICLE{TAJK99,
  author = {Emadeddin Tajkhorshid and Jerome Baudry and Klaus Schulten and Sandor
	Suhai},
  title = {Molecular dynamics study of the nature and origin of retinal's twisted
	structure in bacteriorhodopsin},
  journal = BJ,
  year = {1999},
  note = {In press.}
}

@ARTICLE{TAJK99b,
  author = {E.~Tajkhorshid and B.~Paizs and and S.~Suhai},
  title = {Role of isomerization barriers in the pK(a) control of the retinal
	Schiff base: A density functional study},
  journal = JPC,
  year = {1999},
  volume = {103},
  pages = {4518--4527}
}

@ARTICLE{Thornley,
  author = {J. Thornley and M. Hui and H. Li and T. Cagin and W. Goddard},
  title = {Molecular Dynamics Simulation on Commodity Shared-memory Multiprocessor
	Systems with Lightweight Multithreading},
  journal = {Proceedings of High Performance Computing, 1999 and Advanced Computing
	Technologies Conference},
  year = {1999}
}

@ARTICLE{TIEL99,
  author = {D.~P.~Tieleman and H.~J.~C.~Berendsen and M.~S.~P.~Sansom.},
  title = {An alamethicin channel in a lipid bilayer: molecular dynamics simulations},
  journal = BJ,
  year = {1999},
  volume = {76},
  pages = {1757--1769},
  annote = {uses POPC membrane and Gromacs forcefield}
}

@ARTICLE{TIET99,
  author = {C. Tietz and A. Dr{\"a}benstedt and J. Schuster and J. Wrachtrup},
  title = {Spectroscopy on single light-harvesting complexes at low temperature},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {6328--6333}
}

@ARTICLE{TiBu99,
  author = {I Tinoco and C. Bustamante},
  title = {How RNA Folds},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {293},
  pages = {271--281}
}

@ARTICLE{ToLe99,
  author = {Geza Toth and Craig S. Lent},
  title = {Quasi-Adiabatic Switching for Metal-Island Quantum-Dot Cellular Automata},
  journal = {Journal of Applied Physics},
  year = {1999},
  volume = {85},
  pages = {2977--2984}
}

@ARTICLE{TRIS99,
  author = {H.-W. Trissl and C.J. Law and R.J. Cogdell},
  title = {Uphill energy transfer in {L}{H}2-containing purple bacteria at room
	temperature},
  journal = {Biochim.~Biophys.~Acta},
  year = {1999},
  volume = {1412},
  pages = {149--172}
}

@ARTICLE{Tros99,
  author = {J. Trosset and H.A. Scheraga},
  title = {Prodock: Software Package for Protein Modeling and Docking},
  journal = {J. of Computational Chemistry},
  year = {1999},
  volume = {20},
  pages = {412--427}
}

@ARTICLE{TDST99,
  author = {Thomas M. Truskett and Pablo G. Debenedetti and Srikanth Sastry and
	Salvatore Torquato},
  title = {A single-bond approach to orientation-dependent interactions and
	its implications for liquid water},
  journal = {J.\ Chem.\ Phys.},
  year = {1999},
  volume = {111},
  number = {6}
}

@ARTICLE{VaFB99,
  author = {DB VanGilder and GI Font and ID Boyd},
  title = {{H}ybrid {M}onte {C}arlo particle-in-cell simulation of an ion thruster
	plume},
  journal = {J. of Propulsion and Power},
  year = {1999},
  volume = {15},
  pages = {530--538}
}

@ARTICLE{Viet99,
  author = {M. Visth and J.D. Hirst and B.N. Dominy and H.Daigler and C.L. Brooks},
  title = {Assessing search strategies for flexible docking},
  journal = {J. Computational Chemistry},
  year = {1999},
  volume = {19},
  pages = {1623--1631}
}

@ARTICLE{VOS99,
  author = {M.H. Vos and J.-L. Martin},
  title = {Femtosecond processes in proteins },
  journal = {Biochim.~Biohys.~Acta},
  year = {1999},
  volume = {1411},
  pages = {1--20}
}

@ARTICLE{VULT99,
  author = {S.I.E. Vulto and J.T.M. Kennis and A.M. Streltsov and J. Amesz and
	T.J. Aartsma},
  title = {Energy relaxation within the B850 Absorption band of the isolated
	light-harvesting complex LH2 from {\em {R}hodopseudomonas acidophila}
	at low temperature},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {878--883}
}

@ARTICLE{WEST99,
  author = {W.H.J. Westerhuis and C.N. Hunter and R. van Grondelle and R.A. Niederman},
  title = {Modeling of oligomeric-state dependent spectral heterogeneity in
	the {B}875 light-harvesting complex of {\em {R}hodobacter sphaeroides}
	by numerical simulation},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {7733--7742}
}

@ARTICLE{WILK99,
  author = {K.E. Wilk and S.J. Harpop and L. Jankova and D. Elder and G. Keenan
	and F. Sharples and R.G. Hiller and P.M.G. Curmi},
  title = {Evolution of a light-harvesting protein by addition of new subunits
	and rearrangement of conserved elements: crystal structure of a cryptophyte
	phycoerythrin at 1.63-\AA resolution},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1999},
  volume = {96},
  pages = {8901--8906}
}

@ARTICLE{WILT99,
  author = {W. Wiltschko and R. Wiltschko},
  title = {The effect of yellow and blue light on magnetic compass orientation
	in European robins, {\em {E}rithacus rubecula}},
  journal = {J.~Comp.~Physiol.~A},
  year = {1999},
  volume = {184},
  pages = {295--299}
}

@ARTICLE{WOLL99,
  author = {F.-A. Wollman and L. Minai and R. Nechushtai},
  title = {The biogenesis and assembly of photosynthetic proteins in thylakoid
	membranes},
  journal = {Biochim.~Biohys.~Acta},
  year = {1999},
  volume = {1411},
  pages = {21--85}
}

@ARTICLE{WOOD99,
  author = {Janet M. Wood},
  title = {Osmosensing by bacteria: signals and membrane-based sensors},
  journal = {Microbiology and Molecular Biology Reviews},
  year = {1999},
  pages = {230--262}
}

@ARTICLE{WRIG99,
  author = {Willy Wriggers and Klaus Schulten},
  title = {Investigating a Back Door Mechanism of Actin Phosphate Release by
	Steered Molecular Dynamics},
  journal = PRO,
  year = {1999},
  volume = {35},
  pages = {262--273}
}

@ARTICLE{XuBe99,
  author = {H. Xu and B. J. Berne},
  title = {Multicanonical Jump Walking: A Method for Efficiently Sampling Rough
	Energy Landscapes},
  journal = JCP,
  year = {1999},
  volume = {110},
  pages = {10299--10306},
  number = {21},
  abstract = {The multicanonical sampling and jump walking methods are combined
	to provide a new, effective means of overcoming quasiergodicity in
	{M}onte {C}arlo simulations. In this new method, configurations generated
	during a long multicanonical sampling are stored infrequently and
	a modified jump walking procedure is implemented using this set of
	configurations to sample phase space at low temperature. Multicanonical
	jump walking, as this new method is called, is compared with regular
	jump walking and with straight multicanonical ensemble sampling on
	two systems: a one-dimensional random potential and an Ar-13 cluster.
	It is shown that for the same number of MC steps, the multicanonical
	jump walking method more efficiently samples the phase space than
	either the regular jump walking or the pure multicanonical ensemble
	sampling method.},
  annote = {multicanonical J-walking reference}
}

@ARTICLE{YE99,
  author = {T.~Ye and N.~Friedman and Y.~Gat and G.H.~Atkinson and M.~Sheves
	and M.~Ottolenghi and S.~Ruhman},
  title = {{On the Nature of the Primary Light-Induced Events in Bacteriorhodopsin:
	Ultrafast Spectroscopy of NAtive and C$_{13}$=C$_{14}$ Locked Pigments}},
  journal = JPCB,
  year = {1999},
  volume = {103},
  pages = {5122--5130}
}

@ARTICLE{Yosh99,
  author = {Kenjiro Yoshimura and Ann Batiza and Matt Schroeder and Paul Blount
	and Ching Kung},
  title = {Hydrophilocity of a single residue within {MscL} correlates with
	increased channel mechanosensitivity},
  journal = BJ,
  year = {1999},
  volume = {77},
  pages = {1960--1972}
}

@ARTICLE{Zhan99,
  author = {Hongyu Zhang},
  title = {A new hybrid {M}onte {C}arlo algorithm for protein potential function
	test and structure refinement},
  journal = {Proteins},
  year = {1999},
  volume = {34},
  pages = {464--471}
}

@ARTICLE{ZHAO99,
  author = {Y. Zhao and T. Meier and W.M. Zhang and V. Chernyak and S. Mukamel},
  title = {Superradiance Coherence size in single-molecule spectroscopy of LH2
	antenna complexes},
  journal = {J.~Phys.~Chem.~B},
  year = {1999},
  volume = {103},
  pages = {3954--3962}
}

@INCOLLECTION{BENN98,
  author = {Michal Ben-{N}un and Ferenc Molnar and Hui Lu and James C. Phillips
	and Todd J. {Mart{\'{\i}}nez} and Klaus Schulten},
  title = {Quantum Dynamics of Retinal's Femtosecond Photoisomerization in Bacteriorhodopsin},
  booktitle = {{Faraday Discussions, No. 110}},
  publisher = {Faraday Publications},
  year = {1998},
  pages = {447--462},
  month = DEC,
  annote = {The "Faraday Discussions" homepage is http://www.rsc.org/faraday.}
}

@INCOLLECTION{Bere98,
  author = {H.~J~.C. Berendsen},
  title = {Molecular Dynamics Simulations: The Limits and Beyond},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {3--36},
  month = NOV
}

@INCOLLECTION{DDJS98,
  author = {P. Deuflhard and M. Dellnitz and O. Junge and C. Sch{\"u}tte},
  title = {Computation of Essential Molecular Dynamics by Subdivision Techniques},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {78--97},
  month = NOV
}

@INCOLLECTION{HeMc98,
  author = {V. Helms and J.~A. McCammon},
  title = {Conformational Transitions of Proteins from Atomistic Simulations},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {78--97},
  month = NOV
}

@INCOLLECTION{OkMu97,
  author = {D. Okunbor and R. Murty},
  title = {Parallel Molecular Dynamics Using Force Decomposition},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {483--494},
  month = NOV
}

@INCOLLECTION{PBSB98,
  author = {James C.~Phillips and Robert Brunner and Aritomo Shinozaki and Milind
	Bhandarkar and Neal Krawetz and Attila Gursoy and Laxmikant Kal{\'e}
	and Robert D.~Skeel and Klaus Schulten},
  title = {Avoiding Algorithmic Obfuscation in a Message-Driven Parallel {MD}
	Code},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {455--468},
  month = NOV,
  nack = {This work was supported in part by NIH Grant P41RR05969 and NSF Grants
	BIR-9318159.}
}

@INCOLLECTION{PHIL98,
  author = {James C. Phillips and Robert Brunner and Aritomo Shinozaki and Milind
	Bhandarkar and Neal Krawetz and Laxmikant Kal{\'e} and R.~D. Skeel
	and Klaus Schulten},
  title = {Avoiding Algorithmic Obfuscation in a Message-Driven Parallel {MD}
	Code},
  booktitle = {{Computational Molecular Dynamics: Challenges, Methods, Ideas}},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {472--482},
  month = NOV,
  annote = {This work was supported in part by NIH Grant P41RR05969 and NSF Grants
	BIR-9318159.}
}

@INCOLLECTION{SkIz98,
  author = {R.~D. Skeel and J.~A. Izaguirre},
  title = {The Five Femtosecond Time Step Barrier},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {303--318},
  address = {Berlin Heidelberg New York},
  month = NOV,
  nack = {This work was supported in part by NIH Grant P41RR05969 and NSF Grants
	BIR-9318159 and DMS-9600088.}
}

@MANUAL{BrPS98,
  title = {Extensible Markup Language (XML) 1.0},
  author = {T. Bray and J. Paoli and C. M. Sperberg-McQueen},
  month = OCT,
  year = {1998},
  note = {Downloadable\footnote{http://www.w3.org/TR/1998/REC-xml-19980210.pdf}}
}

@BOOK{MaHD99,
  title = {The Way Life Works: The Science Lover's Illustrated Guide to How
	Life Grows, Develops, Reproduces, and Gets Along},
  publisher = {Crown Publishing Group},
  year = {1998},
  author = {B. Mahlon and M. Hoagland and B. Dodson},
  month = SEP
}

@TECHREPORT{blitz,
  author = {T. Veldhuizen},
  title = {Blitz{++}: The Library That Thinks It Is A Compiler},
  institution = {Extreme! Computing Laboratory, Indiana University Computer Science
	Department},
  year = {1998},
  type = {Conference Presentation},
  month = SEP,
  annote = {\texttt{http://oonumerics.org/blitz/blitztalk.ps.gz}}
}

@INPROCEEDINGS{KALE98,
  author = {L. V. Kale and Milind Bhandarkar and Robert Brunner},
  title = {Load Balancing in Parallel Molecular Dynamics},
  booktitle = {Fifth International Symposium on Solving Irregularly Structured Problems
	in Parallel},
  year = {1998},
  month = AUG
}

@INPROCEEDINGS{KALE98a,
  author = {L. V. Kale and Milind Bhandarkar and Robert Brunner and Joshua Yelon},
  title = {{Multiparadigm, Multilingual Interoperability: Experience with Converse}},
  booktitle = {Proceedings of 2nd Workshop on Runtime Systems for Parallel Programming
	(RTSPP) Orlando, Florida - USA},
  year = {1998},
  series = {Lecture Notes in Computer Science},
  month = MAR
}

@TECHREPORT{DHFS98,
  author = {Peter Deuflhard and Wilhelm Huisinga and Alexander Fischer and Christof
	Sch{\"u}tte},
  title = {Identification of Almost Invariant Aggregates in Reversible Nearly
	Uncoupled {M}arkov Chains},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1998},
  number = {SC 98-03},
  month = FEB
}

@TECHREPORT{SFHD98,
  author = {Christof Sch{\"u}tte and Alexander Fischer and Wilhelm Huisinga and
	Peter Deuflhard},
  title = {A Hybrid {M}onte {C}arlo Method for Essential Molecular Dynamics},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1998},
  number = {SC 98-04},
  month = FEB,
  note = {Available via http://www.zib.de/bib/pub/pw/.}
}

@ARTICLE{DIJK98,
  author = {B. {van Dijk} and J.K.H. Carpenter and A.J. Hoff and P.J. Hore},
  title = {Magnetic field effects on the recombination kinetics of radical pairs},
  journal = {J.~Phys.~Chem.},
  year = {1998},
  volume = {B 102},
  pages = {464--472}
}

@ARTICLE{GuMa98,
  author = {W. F. {van Gunsteren} and A. E. Mark},
  title = {Validation of Molecular Dynamics Simulation},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {108},
  pages = {6109--6116},
  number = {15}
}

@BOOK{Okse98,
  title = {Stochastic Differential Equations: An Introduction with Applications},
  publisher = {Springer-Verlag},
  year = {1998},
  author = {B.~{\O}ksendal},
  edition = {fifth}
}

@ARTICLE{AiTo98,
  author = {Zhuming Ai and Torsten Fr{\"o}hlich},
  title = {Molecular Dynamics Simulation in Virtual Environments},
  journal = {Computer Graphics Forum},
  year = {1998},
  volume = {17},
  pages = {C267--C273},
  number = {3}
}

@ARTICLE{AJOU98,
  author = {Bassam Ajouz and Catherine Berrier and Alexia Garrigues and and Madeleine
	Besnard and Alexandre Ghazi},
  title = {Release of Tioredoxin via the mechanosensitive channel {MscL} during
	osmotic downshock of {\it Escherichia coli} cells},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {26670--26674},
  number = {41}
}

@ARTICLE{ANDR98,
  author = {B. Kim Andrews and Tod Romo and James B. Clarage and B. Montgomery
	Pettitt and George N. Phillips Jr.},
  title = {Characterizing global substates of myoglobin},
  journal = STR,
  year = {1998},
  volume = {6},
  pages = {587--594},
  number = {5}
}

@INPROCEEDINGS{AnBPH98,
  author = {Virgil Andronache and Silvia Brunet and Nelson Passos and Ranette
	Halverson},
  title = {Performance evaluation of parallel implementation of nested loop
	control structures},
  booktitle = {Proc. ISCA 11$^{\mbox{th}}$ International Conf. on Computer Applications
	in Industry and Engineering},
  year = {1998}
}

@ARTICLE{Apos98,
  author = {J. Apostolakis and A. Pluckthun and A. Caflisch},
  title = {Docking small ligands in flexible binding sites},
  journal = {J. Computational Chemistry},
  year = {1998},
  volume = {19},
  pages = {21--37}
}

@ARTICLE{AREL98,
  author = {J.~B.~Arellano and R.~B.~Raju and K.~R.~Naqvi and T.~Gillbro},
  title = {Estimation of Pigment Stoichiometries in Photosynthetic Systems of
	Purple Bacteria - Special Reference to the (Absence of) Second Carotenoid
	in LH2},
  journal = PCPB,
  year = {1998},
  volume = {68},
  pages = {84--87}
}

@ARTICLE{ArRM98,
  author = {A. Arkin and J. Ross and H. H. McAdams},
  title = {Stochastic Kinetic Analysis of Developmental Pathway Bifurcation
	in Phage Lambda-Infected {E}scherichia coli Cells},
  journal = {Genetics},
  year = {1998},
  volume = {149},
  pages = {1633--1648},
  number = {4}
}

@ARTICLE{ARKI98,
  author = {Isaiah T. Arkin and Sergei I. Sukharev and Paul Blount and Ching
	Kung and Axel T. Br{\"u}nger},
  title = {Helicity, membrane incorporation, orientation and thermal stability
	of the large conductance mechanosensitive channel from {{\it E.\,coli}}},
  journal = BBA,
  year = {1998},
  volume = {1369},
  pages = {131--140},
  annote = {First structural studies using FTIR, CD spectra, amide H+/D+ exchange}
}

@ARTICLE{ArTr98,
  author = {S. Artz and S. Trimper},
  title = {Competing {G}lauber and {K}awasaki Dynamics},
  journal = {Int. J. of Modern Phys. B},
  year = {1998},
  volume = {12},
  pages = {2385--2392},
  number = {23}
}

@ARTICLE{Sand98B,
  author = {B. Sandak, H.J. Wolfson and R. Nussinov},
  title = {Flexible docking allowing induced fit in proteins: {I}nsights from
	an open to closed conformational isomers},
  journal = {Proteins: Structure, Function, and Genetics},
  year = {1998},
  volume = {32},
  pages = {159--174}
}

@ARTICLE{BACH98A,
  author = {S.M. Bachilo and C.W. Spangler and T. Gillbro},
  title = {Excited state energies and internal conversion in diphenylpolyenes:
	from diphenylbutadiene to diphenyltetradecaheptaene},
  journal = {Chem.~Phys.~Lett.},
  year = {1998},
  volume = {283},
  pages = {235--242}
}

@ARTICLE{BAIL98,
  author = {Michael Bailey and Klaus Schulten and John E. Johnson},
  title = {The Use of Solid Physical Models for the Study of Macromolecular
	Assembly},
  journal = COSB,
  year = {1998},
  volume = {8},
  pages = {202--208}
}

@ARTICLE{BaCh98,
  author = {Christian Bailly and Jonathan B. Chaires},
  title = {Sequence-specific DNA minor groove binders. Design and synthesis
	of netropsin and distamycin analogues},
  journal = {Bioconjug. Chem.},
  year = {1998},
  volume = {9},
  pages = {513--38},
  number = {5}
}

@ARTICLE{BALA98,
  author = {Alexander Balaeff and Mair E. A. Churchill and Klaus Schulten},
  title = {Structure prediction of a complex between the chromosomal protein
	{HMG-D} and {DNA}},
  journal = PRO,
  year = {1998},
  volume = {30},
  pages = {113--135},
  number = {1}
}

@ARTICLE{BAND98,
  author = {M. Bandilla and B. {\"U}cker and M. Ram and I. Simonin and E. Gelhaye
	and G. McDermott and R.J. Cogdell and H. Scheer},
  title = {Reconstitution of the B800 bacteriochlorophylls in the peripheral
	light harvesting complex B800-850 of {\em {R}hodobacter sphaeroides}
	2.4.1 with BChl $a$ and modified (bacterio-)chlorophylls},
  journal = {Biochim.~Biophys.~Acta},
  year = {1998},
  volume = {1364},
  pages = {390--402}
}

@ARTICLE{BaSc98a,
  author = {Eric Barth and Tamar Schlick},
  title = {Overcoming Stability Limitations in Biomolecular Dynamics. {I}. {C}ombining
	Force Splitting via Extrapolation with {L}angevin Dynamics in {\sc
	ln}},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {109},
  pages = {1617--1632},
  number = {5}
}

@ARTICLE{BaSc98b,
  author = {Eric Barth and Tamar Schlick},
  title = {Extrapolation Versus Impulse in Multiple-Timestepping Schemes. {II}.
	{L}inear Analysis and Applications to {N}ewtonian and {L}angevin
	Dynamics},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {109},
  pages = {1633--1642},
  number = {5}
}

@ARTICLE{BBMZ98,
  author = {D. Bartulewicz and K. Bielawski and A. Markowska and K. Zwierz and
	A. Puckowska and A. Rozanski},
  title = {Synthetic analogues of netropsin and distamycin--synthesis of a new
	pyridine and carbocyclic analogues of the pyrrolecarbocamide antitumour
	antibiobics},
  journal = {Acta. Biochim. Pol.},
  year = {1998},
  volume = {45},
  pages = {41--57},
  number = {1}
}

@ARTICLE{BEHR98,
  author = {Behr, J. and Hellwig, P. and Mantele, W. and Michel, H.},
  title = {Redox Dependent Changes at the Heme Propionates in Cytochrome c Oxidase
	from Paracoccus denitrificans: Direct Evidence from FTIR Difference
	Spectroscopy in Combination with Heme Propionate 13C Labeling},
  journal = {Biochemistry},
  year = {1998},
  volume = {37},
  pages = {7400}
}

@ARTICLE{BENN98A,
  author = {M.~Ben-Nun and T. J. Mart{\'{\i}}nez},
  title = {Nonadiabatic Molecular Dynamics: {Validation} of the Multiple Spawning
	Method for a Multi-Dimensional Problem},
  journal = JCP,
  year = {1998},
  note = {in press}
}

@ARTICLE{BENN98B,
  author = {{Ben-Nun}, M and Mart{\'{\i}}nez, T J},
  title = {{\it Ab initio} Multiple Spawning of Photoinduced cis-trans Isomerization
	in Ethylene},
  journal = {Chem. Phys. Lett.},
  year = {1998},
  volume = {298},
  pages = {57--65}
}

@ARTICLE{BoCB98,
  author = {S. Bogusz and T.~E.~Cheatham III and B. R. Brooks},
  title = {Removal of pressure and free energy artifacts in charged periodic
	systems via net charged corrections to the Ewald potential},
  journal = JCP,
  year = {1998},
  volume = {108},
  pages = {7070--7084},
  annote = {A uniform neutralizing background plasma is employed by default in
	standard Ewald calculations for net-charged systems. We show here
	that this plasma leads to serious artifacts in both system energy
	and pressure, which lead to unrealistic behavior. These artifacts
	are especially critical to simulations where either net charge or
	volume is allowed to change. To correct these problems we institute
	a net-charge correction term that consists of subtracting off the
	Ewald sum for a single particle with charge equal to the net charge
	of the full system and an optional Born or Poisson- Boltzmann term.
	This correction decreases pressure artifacts by three orders of magnitude
	and allows rapid energy convergence as the cell size increases. The
	correction term is general, in that it applies to systems of any
	shape or net charge. The net-charge correction was tested for systems
	in all three phases of matter: gas, solid, and liquid, and found
	to be markedly superior to standard Ewald in all three cases. In
	the gas phase, isolated molecular energies are quickly achieved as
	the cell size increases. In the solid phase the vaporization energy
	of the NaCl crystal is reproduced using free energy perturbation
	techniques where a single atom is removed. In the liquid phase, the
	solvation free energy of Na 1 was investigated. It is demonstrated
	that both the net-charge correction and an energy term twice the
	size of a Born term is required to obtain optimal free energies of
	ionic hydration.}
}

@ARTICLE{BONV98,
  author = {A.~M.~J.~Bonvin and M.~Sunnerhagen and G.~Otting and W.~F.~van Gunsteren.},
  title = {Water molecules in {DNA} recognition {II}: a molecular dynamics view
	of the structure and hydration of the {\em trp} operator},
  journal = JMB,
  year = {1998},
  volume = {282},
  pages = {859--873}
}

@ARTICLE{BRAN98,
  author = {U. Brandt},
  title = {The chemistry and mechanics of ubihydroquinone oxidation at center
	{P} ({Qo}) of the cytochrome bc1 complex},
  journal = BBA,
  year = {1998},
  volume = {1365},
  pages = {261--268}
}

@ARTICLE{BROO98,
  author = {Charles Brooks},
  title = {Simulations of protein folding and unfolding},
  journal = COSB,
  year = {1998},
  volume = {8},
  pages = {222--226}
}

@PHDTHESIS{Bueh98,
  author = {B. B{\"u}hlmann},
  title = {Extensions and Applications of the Graphics Framework {BOOGA}},
  school = {Institute of Computer Science and Applied Mathematics, University
	of Berne},
  year = {1998}
}

@INBOOK{Chan98b,
  chapter = {3},
  pages = {51--66},
  title = {Finding Transition Pathways: Throwing Ropes Over Rough Mountain Passes,
	in the Dark},
  publisher = {World Scientific},
  year = {1998},
  editor = {B.~J. Berne and G. Ciccotti and D.~F. Coker},
  author = {D. Chandler}
}

@ARTICLE{CHAN98,
  author = {G. Chang and R. H. Spencer and A. T. Lee and M. T. Barclay and D.
	C. Rees},
  title = {Structure of the {MscL} homolog from {{\it Mycobacterium tuberculosis}}:
	a gated mechanosensitive ion channel},
  journal = SCI,
  year = {1998},
  volume = {282},
  pages = {2220--2226}
}

@ARTICLE{CORY98,
  author = {Marshall G. Cory and Michael C. Zerner and Xiche Hu and Klaus Schulten},
  title = {Electronic Excitations in Aggregates of Bacteriochlorophylls},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {7640--7650},
  number = {39}
}

@BOOK{Coul97,
  title = {Software Reuse},
  publisher = {Springer Verlag},
  year = {1998},
  author = {B. Coulange},
  address = {London}
}

@ARTICLE{CROF98a,
  author = {Antony R. Crofts and Blanca Barquera and Robert B. Gennis and Richard
	Kuras and Marianna Guergova-Kuras and Edward A. Berry},
  title = {On the mechanism of ubiquinol oxidation by the bc$_1$-complex: {T}he
	different domains of the quinol binding pocket, and their role in
	mechanism, and the binding of inhibitors},
  journal = BCH,
  year = {1998},
  note = {Submitted}
}

@ARTICLE{CROF98c,
  author = {Antony R. Crofts and Edward A. Berry},
  title = {Structure and Function of the Cytochrome $bc_1$ Complex of Mitochondria
	and Photosynthetic Bacteria},
  journal = COSB,
  year = {1998},
  volume = {8},
  pages = {501--509}
}

@ARTICLE{CROF98,
  author = {Antony R. Crofts and Edward A. Berry and Zhaolei Zhang and LiShar
	Huang and Richard Kuras and Marianna Guergova-Kuras},
  title = {On the mechanism of ubiquinol oxidation by the bc$_1$-complex: {T}he
	role of the {R}ieske subunit, and its mobility},
  journal = BCH,
  year = {1998},
  note = {Submitted}
}

@ARTICLE{CROF98b,
  author = {Antony R. Crofts and Sangjin Hong and Zhaolei Zhang and Edward A.
	Berry},
  title = {Physicochemical aspects of the movement of the {R}ieske iron sulphur
	protein during quinol oxidation by $bc_1$ complex from mitochondria
	and photosynthetic bacteria},
  journal = BCH,
  year = {1998},
  note = {Submitted}
}

@ARTICLE{CUEL98,
  author = {Luis G. Cuello and Jesus G. Romero and D. Marien Cortes and Eduardo
	Perozo},
  title = {{pH}-dependent gating in the {\em Streptomyces lividans} {K$^+$}
	channel},
  journal = BCH,
  year = {1998},
  volume = {37},
  pages = {3229--3236},
  number = {10},
  annote = {Concluded that gating is dependent on extracellular residues, but
	this has been contradicted by HEGI99}
}

@ARTICLE{CUNN98,
  author = {F.X. Cunningham and E. Gantt},
  title = {Genes and Enzymes of Carotenoid Biosynthesis in Plants},
  journal = {Annu.~Rev.~Plant Physiol.~Plant Mol.~Biol.},
  year = {1998},
  volume = {49},
  pages = {557--583}
}

@ARTICLE{LEDA98,
  author = {Alexander C. Le Dain and Nathalie Saint and Anna Kloda and Alexandre
	Ghazi and Boris Martinac},
  title = {Mechanosensitive ion channels of the archaeon {\it Haloferax volcanii}},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {12116--12119},
  number = {20}
}

@ARTICLE{DAN98,
  author = {N. Dan and S. A. Safran},
  title = {Effect of lipid characteristics on the structure of transmembrane
	proteins},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {1410--1414}
}

@ARTICLE{DBCC98,
  author = {Christoph Dellago and Peter G. Bolhuis and Felix S. Csajka and David
	Chandler},
  title = {Transition Path Sampling and the Calculation of Rate Constants},
  journal = JCP,
  year = {1998},
  volume = {108},
  pages = {1964--1977},
  number = {5},
  abstract = {We have developed a method to study transition pathways for rare events
	in complex systems. The method can be used to determine rate constants
	for transitions between stable states by turning the calculation
	of reactive flux correlation functions into the computation of an
	isomorphic reversible work. In contrast to previous dynamical approaches,
	the method relies neither on prior knowledge nor on explicit specification
	of transition states. Rather, it provides an importance sampling
	from which transition states can be characterized statistically.
	A simple model is analyzed to illustrate the methodology.}
}

@ARTICLE{DESA98,
  author = {R.Z.B. Desamero and V. Chynwat and I. van der Hoef and F.J. Jansen
	and J. Lugtenburg and D. Gosztola and M.R. Wasielewski and A. Cua
	and D.F. Bocian and H.A. Frank},
  title = {Mechanism of energy transfer from carotenoids to bacteriochlorophyll:
	light-harvesting by carotenoids having different extents of $\pi$-electron
	conjugation incorporated in the {B}850 antenna complex from the carotenoidless
	bacterium {{\em Rhodobacter sphaeroides}} {R}-26.1},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {8151--8162}
}

@ARTICLE{DeHo98,
  author = {M. Deserno and C. Holm},
  title = {How to mesh up {E}wald sums. {I}. {A} theoretical and numerical comparison
	of various particle mesh routines},
  journal = JCP,
  year = {1998},
  volume = {109},
  pages = {7678--7693},
  number = {18},
  annote = {Standard Ewald sums, which calculate, e.g., the electrostatic energy
	or the force in periodically closed systems of charged particles,
	can be efficiently speeded up by the use of the fast Fourier transformation
	(FFT). In this article we investigate three algorithms for the FFT-accelerated
	Ewald sum, which have attracted widespread attention, namely, the
	so-called particle-particle-particle mesh (P3M), particle mesh Ewald
	(PME), and smooth PME method. We present a unified view of the underlying
	techniques and the various ingredients which comprise those routines.
	Additionally, we offer detailed accuracy measurements, which shed
	some light on the influence of several tuning parameters and also
	show that the existing methods - although similar in spirit - exhibit
	remarkable differences in accuracy. We propose a set of combinations
	of the individual components, mostly relying on the P3M approach,
	that we regard to be the most flexible. The issue of estimating the
	errors connected with particle mesh routines is reserved to paper
	II.}
}

@ARTICLE{DICK98,
  author = {R.~E.~Dickerson},
  title = {{DNA} bending: the prevalence of kinkiness and the virtues of normality},
  journal = NAR,
  year = {1998},
  volume = {26},
  pages = {1906--1926}
}

@ARTICLE{DIFF98,
  author = {W.M. Diffey and B.J. Homoelle and M.D. Edington and W.F. Beck},
  title = {Excited state vibrational coherence and anisotropy decay in the bacteriochlorophyll
	$a$ dimer protein {B820}},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {2776--2786}
}

@ARTICLE{DOYL98,
  author = {D.~A.~Doyle and J.~M.~Cabral and R.~A.~Pfuetzer and A.~Kuo and J.~M.~Gulbis
	and S.~L.~Cohen and B.~T.~Chait and R.~Mac{K}innon},
  title = {The structure of the potassium channel: molecular basis of {K}$^+$
	conduction and selectivity},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {69--77},
  annote = {crystal structure for the k channel}
}

@ARTICLE{DCPK98,
  author = {D. A. Doyle and J. M. Cabral and R. A. Pfuetzner and A. Kuo and J.
	M. Gulbis and S. L. Cohen and B. T. Chait and R. MacKinnon},
  title = {The Structure of the Potassium Channel: Molecular Basis of ${K}^+$
	Conduction and Selectivity},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {69--77}
}

@ARTICLE{DUAN98,
  author = {Yong Duan and Peter Kollman},
  title = {Pathways to a protein folding intermediate observed in a 1 microsecond
	simulation in aqueous solution},
  journal = SCI,
  year = {1998},
  volume = {282},
  pages = {740--744}
}

@BOOK{DEKM98,
  title = {Biological Sequence Analysis},
  publisher = {Cambridge University Press},
  year = {1998},
  author = {R. Durbin and S. Eddy and A. Krogh and G. Mitchison}
}

@ARTICLE{EGLI98,
  author = {M.~Egli.},
  title = {Conformational preorganization, hydration, and nucleic acid duplex
	stability},
  journal = {Antisense Nucleic Acid Drug Dev.},
  year = {1998},
  volume = {8},
  pages = {123--128}
}

@ARTICLE{EICH98,
  author = {C. Eichwald and J. Walleczek},
  title = {Magnetic field perturbations as a tool for controlling enzyme-regulated
	and oscillatory biochemical reactions},
  journal = {Biophys.~Chem.},
  year = {1998},
  volume = {74},
  pages = {209--224}
}

@ARTICLE{ESSE98,
  author = {L.O.~Essen and R.~Siegert and W.D.~Lehmann and D.~Oesterhelt},
  title = {{Lipid patches in membrane protein oligomers: Crystal structure of
	the bacteriorhodopsin-lipid complex}},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {11673--11678}
}

@ARTICLE{FEIG98,
  author = {M.~Feig and B.~M.~Pettitt.},
  title = {Crystallographic water sites from a theoretical perspective},
  journal = {Structure},
  year = {1998},
  volume = {6},
  pages = {1351--1354}
}

@ARTICLE{FiCS98,
  author = {Alexander Fischer and Frank Cordes and Christof Sch{\"u}tte},
  title = {{H}ybrid {M}onte {C}arlo with Adaptive Temperature in Mixed-Canonical
	Ensemble: Efficient Conformational Analysis of {RNA}},
  journal = JCC,
  year = {1998},
  volume = {19},
  pages = {1689--1697},
  number = {15}
}

@ARTICLE{For+98,
  author = {G. Forgacs and R.A. Foty and Y. Shafrir and M.S. Steinberg},
  title = {Viscoelastic properties of living tissues: a quantitative study},
  journal = BJ,
  year = {1998},
  volume = {74},
  pages = {2227--2234}
}

@MANUAL{GAUS98,
  title = {Gaussian 98, Revision A7},
  author = {M. J. Frisch and G. W. Trucks and H. B. Schlegel, G. E. Scuseria
	and M. A. Robb and J. R. Cheeseman and V. G. Zakrzewski, J. A. Montgomery
	and R. E. Stratmann and J. C. Burant and S. Dapprich, J. M. Millam
	and A. D. Daniels and K. N. Kudin and M. C. Strain and O. Farkas,
	J. Tomasi and V. Barone and M. Cossi and R. Cammi and B. Mennucci
	and C. Pomelli, C. Adamo and S. Clifford and J. Ochterski and G.
	A. Petersson and P. Y. Ayala, Q. Cui and K. Morokuma and D. K. Malick
	and A. D. Rabuck and K. Raghavachari, J. B. Foresman and J. Cioslowski
	and J. V. Ortiz and B. B. Stefanov and G. Liu and A. Liashenko and
	P. Piskorz and I. Komaromi and R. Gomperts and R. L. Martin, D.~J.
	Fox and T. Keith and M. A. Al-Laham and C. Y. Peng and A. Nanayakkara,
	C. Gonzalez and M. Challacombe and P. M. W. Gill and B. G. Johnson
	and W. Chen, M. W. Wong and J. L. Andres and M. Head-Gordon and E.
	S. Replogle and J. A. Pople},
  organization = {Gaussian Inc.},
  address = {Pittsburgh, PA},
  year = {1998}
}

@MISC{FRIS98,
  author = {Frisch, M. J. and Trucks, G. W. and Schlegel, H. B. and Scuseria,
	G. E. and Robb, M. A. and Cheesman, J. R. and Zakrzewski, V. G. and
	Montgomery Jr., J. A. and Stratmann, R. E. and Burant, J. C. and
	Dapprich, S. and Millam, J. M. and Daniels, A. D. and Kudin, K. N.
	and Strain, M. C. and Farkas, O. and Tomasi, J. and Barone, B. and
	Cossi, M. and Cammi, R.. and Mennucci, B. and Pomelli, C. and Adamo,
	C. and Clifford, S. and Ochterski, J. and Petersson, G. A. and Ayala,
	P. Y. and Cui, Q. and Morokuma, K. and Malick, D. K. and Rabuck,
	A. D. and Raghavachari, K. and Foresman, J. B. and Cioslowski, J.
	and Oritiz, J. V. and Stefanov, B. B. and Liu, G. and Liashenko,
	A. and Piskorz, P. and Komaromi, I. and Gomperts, R. and Martin,
	R. L. and Fox, D.~J. and Keith, T. and Al-Laham, M. A. and Peng,
	C. Y. and Nanayakkara, A. and Gonzalez, C. and Challacombe, M. and
	Gill, P. M. W. and Johnson, B. and Chen, W. and Wong, M. W. and Andres,
	J. L. and Gonzalez, C. and Head-Gordon, M. and Replogle, E. S. and
	Pople, J. A.},
  title = {Gaussian 98, Revision A.1},
  year = {1998},
  publisher = {Gaussian, Inc.}
}

@ARTICLE{FUJI98,
  author = {R. Fujii and K. Onaka and M. Kuki and Y. Koyama and Y. Watanabe},
  title = {The A$_g^-$ energies iff all-trans-neurosporene and spheroidene as
	determined by fluorescence spectroscopy},
  journal = {Chem.~Phys.~Lett.},
  year = {1998},
  volume = {288},
  pages = {847--863}
}

@ARTICLE{GAI98,
  author = {Feng Gai and K.C. Hasson and J. Cooper McDonald and Philip A. Anfinrud},
  title = {{Chemical Dynamics in Proteins: The Photoisomerization of Retinal
	in Bacteriorhodopsin}},
  journal = SCI,
  year = {1998},
  volume = {279},
  pages = {1886--1891}
}

@PHDTHESIS{Gao98,
  author = {G. Gao},
  title = {Large Scale Molecular Simulations with Application to Polymers and
	Nano-scale Materials},
  school = {Caltech},
  year = {1998}
}

@INPROCEEDINGS{GaSS98,
  author = {B. Garc{\'{\i}}a-Archilla and J. M. Sanz-Serna and R.~D. Skeel},
  title = {The Mollified Impulse Method for Oscillatory Differential Equations},
  booktitle = {Numerical Analysis 1997},
  year = {1998},
  editor = {D. F. Griffiths and G. A. Watson},
  pages = {111--123},
  address = {London},
  publisher = {Pitman},
  nack = {Iber, nsf96, nsfarpa, nih},
  nremark = {[Also, Rept.\ No.\ 1997/5, Dept.\ Mat.\ Aplic.\ Comput., Univ.\ de
	Valladolid, Spain, July 1997.]},
  nrights = {to include in other volumes of our own work}
}

@INPROCEEDINGS{GaSS98a,
  author = {B. Garc{\'{\i}}a-Archilla and J. M. Sanz-Serna and R.~D. Skeel},
  title = {The Mollified Impulse Method for Oscillatory Differential Equations},
  booktitle = {Numerical Analysis 1997},
  year = {1998},
  editor = {D. F. Griffiths and G. A. Watson},
  pages = {111--123},
  address = {London},
  publisher = {Pitman},
  nack = {Iber, nsf96, nsfarpa, nih},
  nremark = {[Also, Rept.\ No.\ 1997/5, Dept.\ Mat.\ Aplic.\ Comput., Univ.\ de
	Valladolid, Spain, July 1997.]},
  nrights = {to include in other volumes of our own work}
}

@ARTICLE{GaSS98b,
  author = {B. Garc{\'{\i}}a-Archilla and J. M. Sanz-Serna and R.~D. Skeel},
  title = {Long-Time-Step Methods for Oscillatory Differential Equations},
  journal = SJSC,
  year = {1998},
  volume = {20},
  pages = {930--963},
  number = {3},
  nack = {Iber, nsf96, nsfarpa, nih},
  nremark = {To appear. {[Also Tech. Rept. 1996/7, Dep.\ Math.\ Aplic.\ Comput.,
	Univ. Valladolid, Valladolid, Spain]} Available by anonymous ftp
	from ftp.mac.cie.uva.es as /pub/reports/Report96_7.ps pdf, ps, ps.Z,
	dvi available from http://epubs.siam.org/sam-bin/dbq/article/31385}
}

@ARTICLE{GeLe98,
  author = {M. Gerstein and M. Levitt},
  title = {Simulating Water and the Molecules of Life},
  journal = {Scientific American},
  year = {1998},
  pages = {100--105}
}

@ARTICLE{GoTe98,
  author = {D.~Godt and U.~Tepass},
  title = {{\it Drosophila} oocyte localization is mediated by differential
	cadherin-based adhesion},
  journal = {Nature},
  year = {1998},
  volume = {395},
  pages = {387--391},
  number = {6700}
}

@ARTICLE{GoSt98,
  author = {A.~Gonzalez-Reyes and D.~St. Johnston},
  title = {The {\it {D}rosophila} AP axis is polarised by the cadherin-mediated
	positioning of the oocyte},
  journal = {Development},
  year = {1998},
  volume = {125},
  pages = {3635--3644},
  number = {18}
}

@ARTICLE{GrKS98,
  author = {A. Grama and V. Kumar and A. Sameh},
  title = {Scalable Parallel Formulations Of The {B}arnes-{H}ut Method For {N}-Body
	Simulations},
  journal = JPCP,
  year = {1998},
  volume = {24},
  pages = {797--822},
  number = {5-6}
}

@ARTICLE{GROO98,
  author = {M. Groot and J. Yu and R. Agarwal and J. R. Norris and G. R. Fleming},
  title = {Three-Pulse Photon Echo Measurments on the accessory Pigments in
	the Reaction Center of {\em Rhodobacter sphaeroides}},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {5923--5931}
}

@ARTICLE{GrTa98,
  author = {Helmut Grubm{\"u}ller and Paul Tavan},
  title = {Efficient Algorithms for Molecular Dynamics Simulations of Proteins---How
	Good Are They?},
  journal = JCC,
  year = {1998},
  volume = {19},
  pages = {1534--1552},
  number = {13},
  nremark = {the better performance of method DC-1d is due to more continuity when
	changing distance class; the other methods do nothing special for
	this. Otherwise DC-1d is much like DC-1a, which is a least squares
	fit to DC-1b.}
}

@ARTICLE{GRUE98,
  author = {M. Gruebele and J. Sabelko and R. Ballew and J. Ervin},
  title = {Laser {T}-jump induced protein refolding},
  journal = {Accts. Chem. Res.},
  year = {1998},
  volume = {31},
  pages = {699--707}
}

@ARTICLE{Guns98,
  author = {W. van Gunsteren},
  title = {Validation of Molecular Dynamics Simulation},
  journal = {J. Comput. Phys.},
  year = {1998},
  volume = {108},
  pages = {6109--6116}
}

@INPROCEEDINGS{HaLe98,
  author = {Ernst Hairer and Pierre Leone},
  title = {Order Barriers for Symplectic Multi-value Methods},
  booktitle = {Proceedings of the 17th Dundee Biennial Conference, June 24--27,
	1997},
  year = {1998},
  editor = {D.F. Griffiths and D.J. Higham and G.A. Watson},
  volume = {380},
  series = {Pitman Research Notes in Mathematics},
  pages = {133--149}
}

@ARTICLE{HAMI98,
  author = {J.A.~Hamilton},
  title = {{Fatty acid transport: difficult or easy?}},
  journal = JLR,
  year = {1998},
  volume = {39},
  pages = {467--481},
  number = {3}
}

@ARTICLE{HaTC98,
  author = {S. C. Harvey and R. K. Z. Tan and T. E. Cheatham},
  title = {The Flying Ice Cube---Velocity Rescaling in Molecular Dynamics Leads
	to Violation of Energy Equipartition},
  journal = JCC,
  year = {1998},
  volume = {19},
  pages = {726--740},
  number = {7}
}

@ARTICLE{HEGI98,
  author = {Lise Heginbotham and Ludmila Kolmakova-Partensky and Christopher
	Miller},
  title = {Functional reconstitution of a prokaryotic {K}$^+$ channel},
  journal = JGP,
  year = {1998},
  volume = {111},
  pages = {741--749}
}

@ARTICLE{HERE98,
  author = {J.L. Herek and T. Polivka and T. Pullerits and G.J.S. Fowler and
	C.N. Hunter and V. Sundstrom},
  title = {Ultrafast carotenoid band shifts probe structure and dynamics in
	photosynthetic antenna complexes},
  journal = {Biochem.},
  year = {1998},
  volume = {37},
  pages = {7057--7061}
}

@INCOLLECTION{HERM98,
  author = {Jan Hermans and Geoffrey Mann and Lu Wang and Li Zhang},
  title = {Simulation Studies of Protein-Ligand Interactions},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and R.~D.
	Skeel and S. Reich},
  series = {Lecture Notes in Computational Science and Engineering},
  note = {In press},
  annote = {placement of waters and extraction of xenon from T4-lysozyme L99A}
}

@ARTICLE{Hers98,
  author = {Eli Hershkovitz},
  title = {A Fourth-Order Numerical Integrator for Stochastic {L}angevin Equations},
  journal = {FIXME},
  year = {1998},
  volume = {108},
  pages = {9253--9258},
  number = {22}
}

@ARTICLE{HoLu98,
  author = {Marlis Hochbruck and Christian Lubich},
  title = {A {G}autschi-Type Method for Oscillatory Second-Order Differential
	Equations},
  journal = {Numer.\ Math.},
  year = {1998},
  note = {To appear. Also SFB 382, Report Nr.\ 91, January 1998. Available
	via http://www.am.uni-duesseldorf.de/~marlis/marlispreprints.html}
}

@ARTICLE{HOFA98,
  author = {Ivo Hofacker and Klaus Schulten},
  title = {Oxygen and Proton Pathways in Cytochrome c Oxidase},
  journal = PRO,
  year = {1998},
  volume = {30},
  pages = {100--107},
  number = {1}
}

@ARTICLE{BeLo98,
  author = {B. L. Holian and P. S. Lomdahl},
  title = {Plasticity Induced by Shock Waves in Nonequilibrium Molecular-Dynamics
	Simulations},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {2085--2088}
}

@ARTICLE{HU98,
  author = {Xiche Hu and Ana Damjanovi\'c and Thorsten Ritz and Klaus Schulten},
  title = {Architecture and Function of the Light Harvesting Apparatus of Purple
	Bacteria},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {5935--5941},
  annote = {Invited review.}
}

@ARTICLE{HU98A,
  author = {Xiche Hu and Klaus Schulten},
  title = {A Model for the Light-Harvesting Complex {I (B875)} of {{\em Rhodobacter
	sphaeroides}}},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {683--694}
}

@ARTICLE{HUMP98,
  author = {W. Humphrey and H. Lu and I. Logunov and H. J. Werner and K. Schulten},
  title = {Three Electronic State Model of the Primary Phototransformation of
	Bacteriorhodopsin},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {1689--1699}
}

@ARTICLE{IsNK98,
  author = {H. Ishida and Y. Nagai and A. Kidera},
  title = {Symplectic Integrator for Molecular Dynamics of a Protein in Water},
  journal = {Chem.\ Phys.\ Letts.},
  year = {1998},
  volume = {282},
  pages = {115--120},
  number = {2}
}

@ARTICLE{IWAT98,
  author = {So Iwata and Joong W. Lee and Kengo Okada and John Kyongwon Lee and
	Momi Iwata and Bjarne Rasmussen and Thomas A. Link and S. Ramaswamy
	and Bing K. Jap},
  title = {Complete Structure of the 11-Subunit Bovine Mitochondrial Cytochrome
	$bc_1$ Complex},
  journal = SCI,
  year = {1998},
  volume = {281},
  pages = {64--71}
}

@INCOLLECTION{IZRA98,
  author = {Sergei Izrailev and Sergey Stepaniants and Barry Isralewitz and Dorina
	Kosztin and Hui Lu and Ferenc Molnar and Willy Wriggers and Klaus
	Schulten},
  title = {Steered Molecular Dynamics},
  booktitle = {Computational Molecular Dynamics: Challenges, Methods, Ideas},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. E. Mark and
	S. Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {39--65},
  address = {Berlin}
}

@ARTICLE{JiLG98,
  author = {Y. Jiang and H. Levine and J. A. Glazier},
  title = {Possible Cooperation of Differential Adhesion and Chemotaxis in Mound
	Formation of \emph{Dictyostelium}},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {2615--2625},
  number = {6}
}

@ARTICLE{JOSH98,
  author = {M.~K.~Joshi and S.~Dracheva and A.~K.~Mukhopadhyay and S.~Bose and
	R.~W.~Hendler},
  title = {Importance of specific native lipids in controlling the photocycle
	of Bacteriorhodopsin.},
  journal = {Biochemistry},
  year = {1998},
  volume = {37},
  pages = {14463--14470}
}

@ARTICLE{JUZE98,
  author = {G. Juzeliunas and P. Reineker},
  title = {Pump-probe spectra of linear molecular aggregates: effect of exciton-exciton
	interaction and higher molecular levels},
  journal = JCP,
  year = {1998},
  volume = {109},
  pages = {6916--6928}
}

@ARTICLE{KALG98,
  author = {Amit S. Kalgutkar and Brenda C. Crews and Scott W. Rowlinson and
	Carlos Garner and Karen Seibert and Lawrence J. Marnett},
  title = {{Aspirin-like Molecules that Covalently Inactivate Cyclooxygenase-2}},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {1268--1270}
}

@ARTICLE{KATO98,
  author = {Yasuyuki Kato-Yamada and Hiroyuki Noji and Ryohei Yasuda, Kazuhiko
	Kinosita Jr. and Masasuke Yoshida},
  title = {Direct observation of the rotation of $\epsilon$ subunit in F$_1$-ATPase},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {19375--19377}
}

@ARTICLE{KIM98,
  author = {Hoeon Kim and Di Xia and Chang-An Yu and Jia-Zhi Xia and Anatoly
	M. Kachurin and Li Zhang and Linda Yu and Johann Deisenhofer},
  title = {Inhibitor Binding Changes Domain Mobility in the Iron-Sulphur Protein
	of the Mitochondrial $bc_1$ Complex From Bovine Heart},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {8026--8033}
}

@ARTICLE{KLAH98,
  author = {B.~P.~Klaholz and J.~P.~Renaud and A.~Mitschler and C.~Zusi and P.~Chambon
	and H.~Gronemeyer and D.~Moras},
  title = {Conformational adaptation of agonist to the human nuclear receptor
	RAR${\gamma}$.},
  journal = NATSB,
  year = {1998},
  volume = {5},
  pages = {199--202}
}

@ARTICLE{KOMO98,
  author = {M. Komori and R. Ghosh and S. Takaichi and Y. Hu and T. Mizoguchi
	and Y. Koyama and M. Kuki},
  title = {A null lesion in the rhodopin 3,4-desaturase of {\em {R}hodospirillum
	rubrum} unmasks a cryptic branch of the carotenoid biosynthetic pathway},
  journal = {Biochem.},
  year = {1998},
  volume = {37},
  pages = {8987--8994}
}

@ARTICLE{KOOL98,
  author = {M. H. C. Koolhaas and R. N. Frese and G. J. S. Fowler and T. S. Bibby
	and S. Georgakopoulou and G. {van der Zwan} and C. N. Hunter and
	R. {van Grondelle}},
  title = {Identification of the Upper Exciton Component of the B850 Bacteriochlorophylls
	of the LH2 Antenna Complex, Using a B800-Free Mutant of {\em Rhodobacter
	sphaeroides}},
  journal = BCH,
  year = {1998},
  volume = {37},
  pages = {4693--4698},
  number = {14}
}

@ARTICLE{KRAE98,
  author = {E.T. Kraemer and T. E. Ferrin},
  title = {Molecules to maps: tools for visualization and interaction in support
	of computational biology},
  journal = {Bioinformatics},
  year = {1998},
  volume = {14},
  pages = {764--771},
  number = {9}
}

@ARTICLE{KRUE98,
  author = {B.P. Krueger and G.D. Scholes and R. Jimenez and G.R. Fleming},
  title = {Electronic excitation transfer from carotenoid to bacteriochlorophyll
	in the purple bacterium {{\em Rhodopseudomonas acidophila}}},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {2284--2292}
}

@ARTICLE{KRUE98A,
  author = {B.~P.~Krueger and G.~D.~Scholes and G.~R.~Fleming},
  title = {Calculation of Couplings and Energy-Tranfer Pathways between the
	Pigments of LH2 by the ab Initio Transition Density Cube Method},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {5378--5386}
}

@ARTICLE{LAIB98A,
  author = {P.D. Laible and R.S. Knox and T.G. Owens},
  title = {Detailed balance in F\"orster--Dexter excitation transfer and its
	application to photosynthesis},
  journal = {J.~Phys.~Chem.},
  year = {1998},
  volume = {B 102},
  pages = {1641--1648}
}

@ARTICLE{LAIB98,
  author = {P. D. Laible and V. C. Chynwat and M. C. Thurnauer and M. Schiffer
	and D. K. Hanson and H. A. Frank},
  title = {Protein Modifications Affecting Triplet Energy Transfer in Bacterial
	Photosynthetic Reaction Centers},
  journal = BJ,
  year = {1998},
  volume = {74},
  pages = {2623--2637}
}

@ARTICLE{Lang98,
  author = {D. R. Langley},
  title = {Molecular Dynamic simulations of environment and sequence dependent
	{DNA} conformations: the development of the {BMS} nucleic acid force
	field and comparison with experimental results.},
  journal = {J. Biomol. Struct. Dyn.},
  year = {1998},
  volume = {16},
  pages = {487--509},
  number = {3}
}

@ARTICLE{LEHN98,
  author = {U.~Lehnert and V.~R{\'e}at and M.~Weik and G.~Zacca{\"{\i}} and C.~Pfister},
  title = {Thermal Motions in Bacteriorhodopsin at Different Hydration Levels
	Studied by Neutron Scattering: Correlation with Kinetics and Light-Induced
	Conformational Changes},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {1945--1952}
}

@BOOK{LePa98,
  title = {Elements of the Theory of Computation},
  publisher = {Prentice-Hall},
  year = {1998},
  author = {H.R.~Lewis and C.H.~Papadimitriou},
  address = {Upper Saddle River}
}

@ARTICLE{LEFS98a,
  author = {Jie Liang and Herbert Edelsbrunner and Ping Fu and Pamidighantam
	V. Sudhakar and Shankar Subramaniam},
  title = {Analytical shape computation of macromolecules: {I.} {M}olecular
	area and volume through {A}lpha {S}hape},
  journal = PROlong,
  year = {1998},
  volume = {33},
  pages = {1--17}
}

@ARTICLE{LEFS98b,
  author = {Jie Liang and Herbert Edelsbrunner and Ping Fu and Pamidighantam
	V. Sudhakar and Shankar Subramaniam},
  title = {Analytical shape computation of macromolecules: {II.} {I}naccessible
	cavities in proteins},
  journal = PROlong,
  year = {1998},
  volume = {33},
  pages = {18--29}
}

@ARTICLE{LiEW98,
  author = {Jie Liang and Herbert Edelsbrunner and Clare Woodward},
  title = {Anatomy of protein pockets and cavities: {M}easurement of binding
	site geometry and implications for ligand design},
  journal = PS,
  year = {1998},
  volume = {7},
  pages = {1884--1897}
}

@ARTICLE{LIMA98,
  author = {L. Limantara and R. Fujii and J.-P. Zhang and T, Kaakuno and H. Hara
	and A. Kawamori and T. Yagura and R.J. Cogdell and Y. Koyama},
  title = {Generation of triplet and cation-radical bacteriochlorophyll $a$
	in carotenoidless LH1 and LH2 antenna complexes from {\em {R}hodobacter
	sphaeroides}},
  journal = {Biochem.~},
  year = {1998},
  volume = {37},
  pages = {17469--17486}
}

@ARTICLE{LINN98,
  author = {J. Linnanto and V.M. Helenius and J.A.I. Oksanen and T. Peltola and
	J.-L. Garaud and J.E.I. Korppi-Tommola},
  title = {Exciton interactions and femtosecond relaxation in chlorophyll $a$-water
	and chlorophyll $a$-dioxane aggregates},
  journal = {J.~Phys.~Chem.~A},
  year = {1998},
  volume = {102},
  pages = {4337--4349}
}

@ARTICLE{LSBS98,
  author = {T. Lippert and A. Seyfried and A. Bode and K. Schilling},
  title = {Hyper-systolic parallel computing},
  journal = IEEETPDS,
  year = {1998},
  volume = {9},
  pages = {97--108}
}

@ARTICLE{LU98,
  author = {Hui Lu and Barry Isralewitz and Andre Krammer and Viola Vogel and
	Klaus Schulten},
  title = {Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics
	Simulation},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {662--671}
}

@ARTICLE{LU98A,
  author = {X.~J.~Lu and W.~K.~Olson.},
  title = {Resolving the discrepancies among nucleic acid conformational analysis},
  journal = {FIXME},
  year = {1998},
  note = {In press}
}

@ARTICLE{LUEC98,
  author = {H. L{\"u}cke and H. T. Richter and J. K. Lanyi},
  title = {Proton Transfert Pathways in Bacteriorhodopsin at 2.3 {Angstroms}
	Resolution},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {1934--1937}
}

@ARTICLE{MaKa98,
  author = {J.~Ma and M.~Karplus},
  title = {The allosteric mechanism of the chaperonin {G}ro{EL}: a dynamic analysis},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {8502--8507}
}

@ARTICLE{MA98,
  author = {Y.-Z. Ma and R.J. Cogdell and T. Gillbro},
  title = {Femtosecond energy-transfer dynamics between bacteriochlorophylls
	in the B800-820 Antenna complex of the photosynthetic purple bacterium
	{\em {R}hodopseudomonas acidophila}},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {881--887}
}

@ARTICLE{MaJo98,
  author = {Jennifer I. MacGregor and V. Craig Jordan},
  title = {Basic Guide to the Mechanisms of Antiestrogen Action},
  journal = {Pharmacological Reviews},
  year = {1998},
  volume = {50},
  pages = {151--196},
  number = {2}
}

@ARTICLE{MACH98,
  author = {C. Machado and C.E. Sunkel and D.J. Andrew},
  title = {Human autoantibodies reveal titin as a chromosomal protein},
  journal = JCB,
  year = {1998},
  volume = {141},
  pages = {321--333}
}

@ARTICLE{MACK98,
  author = {A. D. {MacKerell Jr.} and D. Bashford and M. Bellott and R. L. {Dunbrack
	Jr.} and J. Evanseck and M. J. Field and S. Fischer and J. Gao and
	H. Guo and S. Ha and D. Joseph and L. Kuchnir and K. Kuczera and
	F. T. K. Lau and C. Mattos and S. Michnick and T. Ngo and D. T. Nguyen
	and B. Prodhom and I. W. E. Reiher and B. Roux and M. Schlenkrich
	and J. Smith and R. Stote and J. Straub and M. Watanabe and J. {Wiorkiewicz-Kuczera}
	and D. Yin and M. Karplus},
  title = {All-hydrogen empirical potential for molecular modeling and dynamics
	studies of proteins using the {CHARMM22} force field.},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {3586--3616},
  annote = {To cite CHARMM22 field for PROTEINS, cite this paper AND MACK92}
}

@ARTICLE{MACP98A,
  author = {A. Macpherson and T. Gillbro},
  title = {Solvent dependence of the ultrfast S$_2$ -S$_1$ internal conversion
	rate of $\beta$-carotene},
  journal = {J.~Phys.~Chem.~A},
  year = {1998},
  volume = {102},
  pages = {5049--5058}
}

@INPROCEEDINGS{MACP98,
  author = {Alisdair M. Macpherson and Juan B. Arellano and Niall J. Fraser and
	Richard J. Cogdell and Tomas Gillbro},
  title = {Ultrafast energy transfer from rhodopin glucoside in the light harvesting
	complexes of {\em Rps.~acidophila}},
  booktitle = {Photosynthesis: Mechanism and Effects},
  year = {1998},
  editor = {G. Garab},
  volume = {1},
  pages = {9--14},
  publisher = {Kluwer}
}

@BOOK{Mall98,
  title = {Molecular Modelling, Principles and Applications},
  publisher = {Academic Press},
  year = {1998},
  author = {S. Mallat},
  address = {San Diego}
}

@ARTICLE{MARR98,
  author = {Siewert-Jan Marrink and Oliver Berger and Peter Tieleman and Fritz
	J{\"a}hnig},
  title = {Adhesion Forces of Lipids in a Phospholipid Membrane Studied by Molecular
	Dynamics Simulations},
  journal = BJ,
  year = {1998},
  volume = {74},
  pages = {931--943}
}

@ARTICLE{MaHa98,
  author = {T. Matthey and J.~P. Hansen},
  title = {Molecular dynamics simulations of sliding friction in a dense granular
	material},
  journal = {Modelling Simul. Mater. Sci. Eng.},
  year = {1998},
  volume = {6},
  pages = {701--707},
  number = {6},
  annote = {Friction in a dense two-dimensional granular material is studied
	by molecular dynamics simulations. Initially the particles are ordered
	in a triangular lattice where the top layer feels a constant vertical
	pressure and horizontal velocity field. The dynamics of the material
	at low velocities is found to be characterized by avalanche-type
	motion during short time intervals followed by long stationary periods
	of internal stress buildup. At low external pressures, the time-averaged
	shear stress is found to be nearly constant for low values of the
	normal pressure and proportional to the load for higher pressures.}
}

@ARTICLE{Mazu98,
  author = {Alexey K. Mazur},
  title = {Hierarchy of Fast Motions in Protein Dynamics},
  journal = {J. Phys.\ Chem.\ B},
  year = {1998},
  volume = {102},
  pages = {473--479},
  nremark = {540.5 JPC CHX}
}

@ARTICLE{MCMA98,
  author = {B. McMahon and J.D. M{\"u}ller and C.A. Wraight and G.U. Nienhaus},
  title = {Electron Transfer and Protein Dynamics in the Photosynthetic Reaction
	Center},
  journal = {Biophys.~J.},
  year = {1998},
  volume = {74},
  pages = {2567--2587}
}

@BOOK{Merz98,
  title = {Quantum Mechanics},
  publisher = {John Wiley \& Sons},
  year = {1998},
  author = {E. Merzbacher},
  edition = {3rd edition}
}

@ARTICLE{Mitc98,
  author = {W. F. Mitchell},
  title = {The Full Domain Partition Approach to Distributing Adaptive Grids},
  journal = {Applied Numerical Mathematics},
  year = {1998},
  volume = {26},
  pages = {265--275},
  number = {8}
}

@ARTICLE{MIYA98,
  author = {Y. Miyamoto and A. Sancar},
  title = {Vitamin {B}$_2$-based blue-light photoreceptors in the retinohypothalamic
	tract as the photoactive pigments for setting the circadian clock
	in mammals},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1998},
  volume = {95},
  pages = {6097--6102}
}

@ARTICLE{MOE98,
  author = {Paul C. Moe and Paul Blount and Ching Kung},
  title = {Functional and structural conservation in the mechanosensitive channel
	{MscL} implicates elements crucial for mechanosensation},
  journal = {Molecular Microbiology},
  year = {1998},
  volume = {28},
  pages = {583--592},
  number = {3}
}

@ARTICLE{MOHT98,
  author = {N. Mohtat and F.L. Cozens and T. Hancock-Chen and J.C. Scaiano and
	J. McLean and J. Kim},
  title = {Magnetic field effects on the behaviour of radicals in protein and
	{D}{N}{A} environment},
  journal = {Photochem.~Photobiol.},
  year = {1998},
  volume = {67},
  pages = {111--118}
}

@ARTICLE{MONS98,
  author = {R. Monshouwer and A. Baltuska and F. {van Mourik} and R. {van Grondelle}},
  title = {Time-resolved absorption difference spectroscopy of the LH-1 antenna
	of {\em {R}hodopseudomonas viridis}},
  journal = {J.~Phys.~Chem.},
  year = {1998},
  volume = {102},
  pages = {4360--4371}
}

@ARTICLE{NAQV98,
  author = {K.R. Naqvi and R.S. Knox},
  title = {Comment on "Anisotropy in the transient absorption change of a molecular
	system with two-dimensionally degenerate transitions},
  journal = {Phys.~Rev.~A},
  year = {1998},
  volume = {58},
  pages = {3360--3361}
}

@ARTICLE{NOLT98,
  author = {R.~T.~Nolte and G.~B.~Wisley and S.~Westin and J.~E.~Cobb and M.~H.~Lambert
	and R.~Kurokawa and M.~G.~Rosenfeld and T.~M.~Willson and C.~K.~Glass
	and M.~V.~Milburn},
  title = {Ligand binding and co-activator assembly of the peroxisome proliferator-activated
	receptor-${\gamma}$.},
  journal = Nat,
  year = {1998},
  volume = {395},
  pages = {137--143},
  annote = {2.2A resolution}
}

@ARTICLE{OBER98,
  author = {Andres F. Oberhauser and Piotr E. Marszalek and Harold Erickson and
	Julio Fernandez},
  title = {The molecular elasticity of tenascin, an extracellular matrix protein},
  journal = NAT,
  year = {1998},
  volume = {393},
  pages = {181--185}
}

@ARTICLE{VANO98,
  author = {A.M. van Oijen and M. Ketelaars and J. K\"{o}hler and T.J. Aartsma
	and J. Schmidt},
  title = {Spectroscopy of single light-harvesting complexes from purple photosynthetic
	bacteria at 1.2 K},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {9363--9366}
}

@ARTICLE{OSTR98,
  author = {J.~Ostrowski and T.~Roalsvig and L.~Hammer and A.~Marinier and J.~E.~Starret
	Jr. and K.~L.~Yu and P.~R.~Reczek},
  title = {Serine 232 and Methionine 272 Define the Ligand Binding Pocket in
	Retinoic Acid Receptor Subtypes},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {3490--3495}
}

@ARTICLE{OU98,
  author = {Xiaorong Ou and Paul Blount and Robert J. Hoffman and Ching Kung},
  title = {One face of a transmembrane helix is crucial in mechanosensitive
	channel gating},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {11471--11475}
}

@ARTICLE{PaHF98,
  author = {I Pagonabarraga and M H J Hagen and D Frenkel},
  title = {Self-Consistent Dissipative Particle Dynamics Algorithm},
  journal = EPL,
  year = {1998},
  volume = {42},
  pages = {377--382},
  number = {4}
}

@ARTICLE{PGTR98,
  author = {V. Pande and A. Grosberg and T. Tanaka and D. Rokhsar},
  title = {Pathways for protein folding: is a new view needed?},
  journal = COSB,
  year = {1998},
  volume = {8},
  pages = {68--79}
}

@ARTICLE{PATE98,
  author = {Ananda J. Patel and Eric Honor{\'e} and Fran{\c c}ois Maingret and
	Florian Lesage and Michel Fink and Fabrice Duprat and Michel Lazdunski},
  title = {A mammalian two pore domain mechano-gated {S}-like {K$^+$} channel},
  journal = EMBO,
  year = {1998},
  volume = {17},
  pages = {4283--4290},
  number = {15}
}

@ARTICLE{PHEN98,
  author = {Jennifer Phend and Linsen Bai and Ferenc Molnar and Klaus Schulten},
  title = {Ising Spins on Regular Bodies: {A}nalytical Theory, Computer Simulation,
	and Application to Viral Infection, Fever and Vaccines},
  journal = AJP,
  year = {1998},
  note = {Submitted.}
}

@ARTICLE{PiVH98,
  author = {C.\ Picioreanu and M.\ C.\ M.\ van Loosdrecht and J.\ J.\ Heijnen},
  title = {A New Combined Differential-Discrete Cellular Automaton Approach
	for Biofilm Modeling; Application for Growth in Gel Beads},
  journal = {Biotechnl. Bioeng.},
  year = {1998},
  volume = {57},
  pages = {718--731}
}

@ARTICLE{PILC98,
  author = {M. Pilch and M. Pawlikowski},
  title = {Circular Dichroism ({CD}) study of Peridinin-Chlorophyll {\em a}
	Protein ({PCP}) Complexes from Marine Dinoflagellate Algae},
  journal = JCS # { - Faraday Transactions},
  year = {1998},
  volume = {94},
  pages = {227--232},
  number = {2}
}

@ARTICLE{PLIM98,
  author = {S. Plimpton and S. Attaway and B. Hendrickson and J. Swegle and C.
	Vaughan and D. Gardner},
  title = {Parallel Transient Dynamics Simulations: Algorithms For Contact Detection
	And Smoothed Particle Hydrodynamics},
  journal = JPDC,
  year = {1998},
  volume = {50},
  pages = {104--122},
  number = {1-2}
}

@ARTICLE{POTM98,
  author = {E.O. Potma and D.A. Wiersma},
  title = {Exciton superradiance in aggregates: the effect of disorder, higher
	order exciton-phonon coupling and dimensionality},
  journal = JCP,
  year = {1998},
  volume = {108},
  pages = {4894--4903}
}

@ARTICLE{PrMM98,
  author = {P. Procacci and M. Marchi and G.~J. Martyna},
  title = {Electrostatic calculations and multiple time scales in molecular
	dynamics simulation of flexible molecular systems},
  journal = JCP,
  year = {1998},
  volume = {108},
  pages = {8799--8803},
  number = {21},
  annote = {n this paper, we deal with the handling of the electrostatic forces
	in complex molecular systems. In particular, we focus on instabilities
	experienced by reversible multiple time step algorithms when used
	in conjunction with Ewald summation techniques for periodic systems.
	We show that energy conservation is negatively affected by the intra-molecular
	energy term due to electrostatic excluded contacts required by the
	most frequently used of the modern force fields for biomolecular
	systems. These effects are due to a non-complete cancellation of
	the intra-molecular electrostatic energy and forces at intermediate
	or long time steps.}
}

@ARTICLE{PUGH98,
  author = {R.J. Pugh and P. McGlynn and M.R. Jones and C.N. Hunter},
  title = {The LH1\_RC core complex of {\em {R}hodobacter sphaeroides}: interaction
	between components, time-dependent assembly, and topology of the
	PufX protein},
  journal = {Biochim.~Biophys.~Acta},
  year = {1998},
  volume = {1366},
  pages = {301--316}
}

@ARTICLE{PuKo98,
  author = {M. P{\"u}tz and A. Kolb},
  title = {Optimization Techniques for Parallel Molecular Dynamics Using Domain
	Decomposition},
  journal = {Computer Phys.\ Comms.},
  year = {1998},
  volume = {113},
  pages = {145--167},
  number = {2 and 3},
  nremark = {510.8405 COP PHX}
}

@MISC{VRPN,
  author = {{R. M. Taylor II}},
  title = {{VRPN}: {V}irtual {R}eality {P}eripheral {N}etwork},
  year = {1998},
  note = {{\tt http://www.cs.unc.edu/Research/vrpn/}}
}

@ARTICLE{RECC98,
  author = {P.A. Recchia and C.M. Davis and T.G. Lilburn and J.T. Beatty and
	P.S. Parkes-Loach and C.N. Hunter and P.A. Loach},
  title = {Isolation of the {P}uf{X} protein from {\em {R}hodobacter capsulatus}
	and {\em {R}hodobacter sphaeroides}: evidence for its interaction
	with the $\alpha$-polypeptide of the core light-harvesting complex},
  journal = {Biochem.~},
  year = {1998},
  volume = {37},
  pages = {11055--11063}
}

@MISC{Reic98,
  author = {S. Reich},
  title = {Dynamical systems, numerical integration, and exponentially small
	estimates},
  year = {1998},
  note = {Habilitation Thesis},
  nremark = {includes the symplectic variable step-size approach},
  school = {Free University Berlin}
}

@ARTICLE{RIEF98B,
  author = {M. Rief and J. Fernandez and H. Gaub},
  title = {Elasticity coupled two-level systems as a model for biopolymer extensibility},
  journal = PRL,
  year = {1998},
  volume = {81},
  pages = {4764--4767}
}

@ARTICLE{RIEF98,
  author = {Matthias Rief and Mathias Gautel and Alexander Schemmel and Hermann
	Gaub},
  title = {The mechanical Stability of Immunoglobulin and Fibronectin {III}
	Domains in the Muscle Protein Titin Measured by AFM},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {3008--3014}
}

@INPROCEEDINGS{RITZ98A,
  author = {Thorsten Ritz and Ana Damjanovi\'c and Klaus Schulten},
  title = {Light-Harvesting and Photoprotection by Carotenoids: {S}tructure-Based
	Calculations for Photosynthetic Antenna Systems},
  booktitle = {Photosynthesis: {M}echanisms and Effects ({P}roceedings of the {XIth}
	International Congress on Photosynthesis)},
  year = {1998},
  editor = {G. Garab},
  volume = {1},
  pages = {487--490},
  address = {Dordrecht},
  publisher = {Kluwer Academic Publications}
}

@ARTICLE{RITZ98B,
  author = {Thorsten Ritz and Ana Damjanovi\'c and Klaus Schulten},
  title = {Electronic Excitation Transfer Between Carotenoids and Bacteriochlorophylls
	in a Light-Harvesting Protein},
  journal = PRL,
  year = {1998},
  note = {Submitted.}
}

@ARTICLE{RITZ98,
  author = {Thorsten Ritz and Xiche Hu and Ana Damjanovi\'c and Klaus Schulten},
  title = {Excitons and Excitation Transfer in the Photosynthetic Unit of Purple
	Bacteria},
  journal = {Journal of Luminescence},
  year = {1998},
  volume = {76-77},
  pages = {310--321},
  annote = {The article appears in the DPC `97 Proceedings being published in
	the journal}
}

@ARTICLE{RoKS98,
  author = {A. Rojnuckarin and S. Kim and S. Subramaniam},
  title = {Brownian Dynamics Simulations of Protein Folding: Access to Milliseconds
	Time Scale and Beyond},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1998},
  volume = {95},
  pages = {4288--4292}
}

@ARTICLE{ROTH96,
  author = {D.M. Rothwarf and Harold A. Scheraga},
  title = {Role of non-native aromatic and hydrophobic interactions in the folding
	of hen egg white lysozyme},
  journal = BCH,
  year = {1998},
  volume = {35},
  pages = {13797--13807}
}

@ARTICLE{RuBr98,
  author = {R.E. Rudd and J.Q. Broughton},
  title = {Coarse-grained molecular dynamics and the atomic limit of finite
	elements},
  journal = PRB,
  year = {1998},
  volume = {58},
  pages = {5893--5896},
  number = {10}
}

@ARTICLE{REAT98,
  author = {V.~R{\'e}at and H.~Patzelt and M.~Ferrand and C.~Pfister and D.~Oesterhelt
	and G.~Zacca{\"{\i}}},
  title = {Dynamics of diferent parts of bacteriorhodopsin: {H-$^2$H} exchange
	and neutron scattering},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {4970--4975}
}

@INCOLLECTION{SACH98,
  author = {F. Sachs and C. Morris},
  title = {Mechanosensitive ion channels in non-specialized cells},
  booktitle = {Reviews of Physiology and Biochemistry and Pharmacology},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {M.P. Blaustein and R. Greger and H. Grunicke and R. Jahn and L.J.
	Mendell and A. Miyajima and D. Pette and G. Schultz and M. Schweiger},
  pages = {1--78},
  address = {Berlin},
  annote = {Eukaryotic MS channels require coupling to cytoskeleton or extracellular
	matrix}
}

@ARTICLE{SaMo98a,
  author = {R. Samudrala and J. Moult},
  title = {A Graph-Theoretic Algorithm for Comparative Modelling of Protein
	Structure},
  journal = {J. Mol. Biol.},
  year = {1998},
  volume = {279},
  pages = {287--302}
}

@ARTICLE{SaMo98b,
  author = {R. Samudrala and J. Moult},
  title = {Determinants of Side Chain Conformational Preferences in Protein
	Structures},
  journal = {Protein Eng.},
  year = {1998}
}

@ARTICLE{SaMa98,
  author = {S. O. Samuelson and G. J. Martyna},
  title = {Two dimensional umbrella sampling techniques for the computer simulation
	study of helical peptides at thermal equilibrium: The 3{K}(I) peptide
	in vacuo and solution},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {109},
  pages = {11061--11073},
  number = {24}
}

@ARTICLE{Sand98,
  author = {B. Sandak and R. Nussinov and H.J. Wolfson},
  title = {A Method for Biomolecular Structural Recognition and Docking Allowing
	Conformational Flexibility},
  journal = {J. Computational Biology},
  year = {1998},
  volume = {5},
  pages = {631--654}
}

@ARTICLE{SaNW98,
  author = {Bilha Sandak and Ruth Nussinov and Haim J. Wolfson},
  title = {A method for biomolecular and structural recognition and docking
	allowing conformational flexibility},
  journal = {Journal of Computational Biology},
  year = {1998},
  volume = {5},
  pages = {631--654},
  number = {4}
}

@ARTICLE{SaWN98,
  author = {Bilha Sandak and Haim J. Wolfson and Ruth Nussinov},
  title = {Flexible docking allowing induced fit in proteins: Insights from
	an open to closed conformational isomers},
  journal = PROlong,
  year = {1998},
  volume = {32},
  pages = {159--174},
  number = {2}
}

@INCOLLECTION{Schl98,
  author = {Tamar Schlick},
  title = {Some Failures and Successes of Long-Timestep Approaches to Biomolecular
	Simulations},
  booktitle = {Algorithms for Macromolecular Modelling},
  publisher = {Springer-Verlag},
  year = {1998},
  editor = {P. Deuflhard and J. Hermans and B. Leimkuhler and A. Mark and S.
	Reich and R.~D. Skeel},
  volume = {4},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {221--250}
}

@ARTICLE{SMSS98,
  author = {Tamar Schlick and Margaret Mandziuk and Robert D. Skeel and K. Srinivas},
  title = {Nonlinear Resonance Artifacts in Molecular Dynamics Simulations},
  journal = {J. Comput.\ Phys.},
  year = {1998},
  volume = {139},
  pages = {1--29},
  nack = {nsf96, nih, nsf/arpa}
}

@ARTICLE{Schn98b,
  author = {V. Schnecke and C.A. Swanson and E.D. Getzoff and J.A. Tainer and
	L.A. Kuhn},
  title = {Screening a Peptidyl Database for Potential Ligands to Proteins With
	Side-Chain Flexibility},
  journal = {Proteins: Structure, Function, and Genetics},
  year = {1998},
  volume = {33},
  pages = {74--87}
}

@ARTICLE{SCHN98,
  author = {B.~Schneider and K.~Patel and H.~M.~Berman.},
  title = {Hydration of the phosphate group in double helical {DNA}},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {2422--2434}
}

@TECHREPORT{SBHK98,
  author = {Klaus Schulten and Gila Budescu and William Humphrey and Laxmikant
	V. Kale},
  title = {Collaboratory for Structural Biology},
  institution = {University of Illinios at Urbana-Champaign},
  year = {1998},
  type = {Research Proposal},
  address = {University of Illinois at Urbana-Champaign, 405 North Matthews Avenue,
	Urbana, IL 61801},
  annote = {A funded proposal for BioCoRE, an MD collaboratory set up from the
	University of Illinios at Urbana-Champaign. The BioCoRE collaboratory
	allows for utilization of centrally located tools, keeping records,
	and communicating with collaborators, amongst other things.}
}

@ARTICLE{SHIL98,
  author = {Julian Shillcock and Udo Seifert},
  title = {Escape from a metastable well under a time-ramped force},
  journal = PRE,
  year = {1998},
  volume = {57},
  pages = {7301--7304},
  number = {6}
}

@ARTICLE{SHUI98,
  author = {X.~Shui and L.~McFail-Isom and G.~G.~Hu and L.~D.~Williams.},
  title = {The {B--DNA} dodecamer at high resolution reveals a spine of water
	on sodium},
  journal = BCH,
  year = {1998},
  volume = {37},
  pages = {8341--8355}
}

@ARTICLE{SHUI98A,
  author = {X.~Shui and C.~C.~Sines and L.~McFail-Isom and D.~VanDerveer and
	L.~D.~Williams.},
  title = {Structure of the potassium form of {CGCGAATTCGCG:DNA} deformation
	by electrostatic collapse around inorganic cations},
  journal = BCH,
  year = {1998},
  volume = {37},
  pages = {16877--16887}
}

@INPROCEEDINGS{SiLu98,
  author = {J.~G. Siek and A. Lumsdaine},
  title = {The {M}atrix {T}emplate {L}ibrary: A unifying framework for numerical
	linear algebra},
  booktitle = {International Symposium on Computing in Object-Oriented Parallel},
  year = {1998},
  series = {Parallel Object Oriented Scientific Computing},
  organization = {ECOOP},
  annote = {Also available from {\tt http://www.lsc.nd.edu/downloads/research/mtl/papers/mtl\_poosc.pdf}}
}

@ARTICLE{Skee98,
  author = {R.~D. Skeel},
  title = {Comments on `{N}umerical Instability due to Varying Time Steps in
	Explicit Wave Propagation and Mechanics Calculations' by {J}oseph~{P}.
	{W}right},
  journal = {J. Comput.\ Phys.},
  year = {1998},
  volume = {145},
  pages = {758--759}
}

@ARTICLE{SMIT98,
  author = {G.~R. Smith and M.~S.~P. Sansom.},
  title = {Dynamic properties of {N}a$^+$ ions in models of ion channels: {A}
	molecular dynamics study},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {2767--2782},
  annote = {calculates diffusion coefficients of a sodium ion through model ion
	channels}
}

@ARTICLE{SO98,
  author = {On-Yee So and Liliana E. Scarafia and Amy Y. Mak and Ondine H. Callan
	and David C. Swinney},
  title = {The Dynamics of Prostaglandin {H} Synthases},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {5801--5807},
  number = {10}
}

@ARTICLE{SOMS98,
  author = {O.J.G. Somsen and V. Chernyak and R.N. Frese and R. van Grondelle
	and S. Mukamel},
  title = {Excitonic interactions and {S}tark spectroscopy of light harvesting
	systems},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {8893--8908}
}

@ARTICLE{SONG98,
  author = {L. Song and M.A. El-Sayed},
  title = {{Primary Step in Bacteriorhodopsin Photosynthesis: Bond Stretch Rather
	than Angle Twist of Its Retinal Excited-State Structure}},
  journal = JACS,
  year = {1998},
  volume = {120},
  pages = {8889--8890},
  number = {34}
}

@ARTICLE{STEI98,
  author = {M. S. Steinberg},
  title = {Goal-directedness in embryonic development},
  journal = {Integrative Biology},
  year = {1998},
  volume = {1},
  pages = {49--59}
}

@ARTICLE{STRE98,
  author = {A.M. Streltsov and S.I.E. Vulto A.Y. Shkuropatov and A.J. Hoff and
	T.J. Aartsma and V.A. Shuvalov},
  title = {B$_A$ and {B}$_B$ absorbance perturbations induced by coherent nuclear
	motions in reaction centers from {\em {R}hodobacter sphaeroides}
	upon 30-fs excitation of the primary donor},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {7293--7298}
}

@ARTICLE{STUR98,
  author = {J.N. Sturgis and A. Gall and A. Ellervee and A. Freiberg and B. Robert},
  title = {The effect of pressure on the bacteriochlorophyll $a$ binding sites
	of the core antenna complex from {\em {R}hodospirillum rubrum}},
  journal = {Biochem.},
  year = {1998},
  volume = {37},
  pages = {14875--14880}
}

@ARTICLE{SUNN98,
  author = {M.~Sunnerhagen and V.~P.~Denisov and K.~Venu and A.~M~.J~.~J.~Bonvin
	and J.~Carey and B.~Halle and G.~Otting.},
  title = {Water molecules in {DNA} recognition {I}: hydration lifetimes of
	{\em trp} operator {DNA} in solution measured by {NMR} spectroscopy},
  journal = JMB,
  year = {1998},
  volume = {282},
  pages = {847--858}
}

@ARTICLE{TANE98,
  author = {D.~M.~Tanenbaum and Y.~Wang and S.~P.~Williams and P.~B.~Sigler},
  title = {Crystallographic comparison of the estrogen and progesterone receptor's
	ligand binding domains.},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {5998--6003}
}

@ARTICLE{TEMP98,
  author = {Richard H. Templer and Saffron J. Castle and A. Rachael Curran and
	Garry Rumbles and David R. Klug},
  title = {Sensing isothermal changes in the lateral pressure in model membranes
	using di-pyrenyl phosphatidylcholine},
  journal = {Faraday Discussions},
  year = {1998},
  volume = {111},
  pages = {41--53}
}

@ARTICLE{TIMM98A,
  author = {C.R. Timmel and C.E. Fursman and A.J. Hoff and P.J. Hore},
  title = {Spin-correlated radical pairs: microwave pulse effects on lifetimes,
	electron spin echo envelope modulations, and optimum conditions for
	detection by electron spin echo spectroscopy},
  journal = {Chem.~Phys.},
  year = {1998},
  volume = {226},
  pages = {271--283}
}

@ARTICLE{TIMM98,
  author = {C.R. Timmel and U. Till and B. Brocklehurst and K.A. McLauchlan and
	P.J. Hore},
  title = {Effects of weak magnetic fields on free radical recombination reactions},
  journal = {Mol.\ Phys.},
  year = {1998},
  volume = {95},
  pages = {71--89},
  annote = {Good theoretical analysis of weak magnetic field effect}
}

@ARTICLE{TSAI98,
  author = {A.~Tsai and G.~Palmer and G.~Xiao and D.C.~Swinney and R.J.~Kulmacz},
  title = {{Structural Characterization of Arachidonyl Radicals Formed by Prostaglandin
	H Synthase-2 and Prostaglandin H Synthase-1 Reconstituted with Mangano
	Protoporphyrin IX}},
  journal = JBC,
  year = {1998},
  volume = {273},
  pages = {3888--3894},
  number = {7}
}

@ARTICLE{TZON97,
  author = {Svilen Tzonev and Joseph Malpeli and Klaus Schulten},
  title = {A three-dimensional model of the morphogenesis of the Rhesus lateral
	geniculate nucleus},
  journal = {Journal of computational neuroscience},
  year = {1998},
  note = {In press.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{VOMB98,
  author = {E.~Vombaur and M.~Harbers and S.~J.~Um and A.~Benecke and P.~Chambon
	and R.~Losson.},
  title = { The yeast {ADA} complex mediates the ligand--dependent activation
	function {AF}-2 of Retinoid {X} and Estrogen Receptors},
  journal = GAD,
  year = {1998},
  volume = {12},
  pages = {1278--1289}
}

@ARTICLE{WADE98,
  author = {Rebecca C. Wade and Razif R. Gabdoulline and Susanna K. Ludemann
	and Valere Lounnas},
  title = {Electrostatic steering and ionic tethering in enzyme-ligand binding:
	Insights from simulations},
  journal = PNAS,
  year = {1998},
  volume = {95},
  pages = {5942--5949}
}

@ARTICLE{WANG98,
  author = {Hongyun Wang and George Oster},
  title = {Energy Transduction in the {F$_1$} Motor of {ATP} synthase},
  journal = NAT,
  year = {1998},
  note = {In press.},
  annote = {ATPase motor}
}

@ARTICLE{WILL98X,
  author = {Oscar H. Willemsen and Margot M. E. Snel and Kees O. van der Werf
	and Bart G. de Grooth and Jan Greve and Peter Hinterdorfer and Hermann
	J. Gruber and Hansgeorg Schindler and Yvette van Kooyk and Carl G.
	Figdor},
  title = {Simultaneous Height and Adhesion Imaging of Antibody-Antigen Interactions
	by Atomic Force Microscopy},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {2220--2228}
}

@ARTICLE{WILL98,
  author = {S.~P.~Williams and P.~B.~Sigler},
  title = {Atomic structure of progesterone complexed with its receptor.},
  journal = NAT,
  year = {1998},
  volume = {393},
  pages = {392--396}
}

@ARTICLE{WODA98,
  author = {J.~Woda and B.~Schneider and K.~Patel and K.~Mistry and H.~M.~Berman},
  title = {An analysis of the relationship between hydration and protein--DNA
	interactions},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {2170--2177}
}

@ARTICLE{WRIG98B,
  author = {Willy Wriggers and Ernest Mehler and Felicia Pitici and Harel Weinstein
	and Klaus Schulten},
  title = {Structure and Dynamics of Calmodulin in Solution},
  journal = BJ,
  year = {1998},
  volume = {74},
  pages = {1622--1639}
}

@ARTICLE{WRIG98C,
  author = {Willy Wriggers and Ronald A. Milligan and Klaus Schulten and J. Andrew
	McCammon},
  title = {Self-Organizing Neural Networks Bridge the Biomolecular Resolution
	Gap},
  journal = JMB,
  year = {1998},
  volume = {284},
  pages = {1247--1254}
}

@ARTICLE{WRIG98A,
  author = {Willy Wriggers and Klaus Schulten},
  title = {Nucleotide-dependent movements of the kinesin motor domain predicted
	by simulated annealing},
  journal = BJ,
  year = {1998},
  volume = {75},
  pages = {646--661}
}

@ARTICLE{Wrig98,
  author = {Joseph P. Wright},
  title = {Numerical Instability Due to Varying Time Steps in Explicit Wave
	Propagation and Mechanics Calculations},
  journal = {J. Comput.\ Phys.},
  year = {1998},
  volume = {140},
  pages = {421--431},
  number = {2}
}

@ARTICLE{WU98,
  author = {H.M. Wu and G.J. Small},
  title = {Symmetry-based analysis of the effects of random energy disorder
	on the excitonic level structure of cyclic arrays: Application to
	photosynthetic antenna complexes},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {888--898}
}

@ARTICLE{WU98A,
  author = {Xiongwu Wu and Shaomeng Wang},
  title = {{Self-Guided Molecular Dynamics Simulation for Efficient Conformational
	Search}},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {7238--7250},
  number = {37}
}

@ARTICLE{YANG98,
  author = {Cheng Y. Yang and Klaus Schulten and Charles Pidgeon},
  title = {Molecular Dynamics Simulations of Bile Salts and Immobilized Artifical
	Membranes},
  journal = JPC,
  year = {1998},
  note = {Submitted.}
}

@ARTICLE{YoST98,
  author = {S. Yoshikawa and K. Shinzawa-Itoh and T. Tsukihara},
  title = {Crystal Structure of Bovine Heart Cytochrome c Oxidase at 2.8A Resolution},
  journal = JBB,
  year = {1998},
  volume = {30},
  pages = {7},
  abstract = {Thirteen different polypeptide subunits, each in one copy, five phosphatidyl
	ethanolamines and three phosphatidyl glycerols, two hemes A, three
	Cu ions, one Mg ion, and one Zn ion are detectable in the crystal
	structure of bovine heart cytochrome c oxidase in the fully oxidized
	form at 2.8 Angstrom resolution. A propionate of hems a, a peptide
	unit (-CO-NH-), and an imidazole bound to Cu-A are hydrogen-bonded
	sequentially, giving a facile electron transfer path from Cu-A to
	heme a. The O-2 binding and reduction site, heme a(3), is 4.7 Angstrom
	apart from Cu-B. Two possible proton transfer paths from the matrix
	side to the cytosolic side are located in subunit I, including hydrogen
	bonds and internal cavities likely to contain randomly oriented water
	molecules. Neither path includes the O-2 reduction site. The O-2
	reduction site has a proton transfer path from the matrix side possibly
	for protons for producing water. The coordination geometry of Cu-B
	and the location of Tyr(244) in subunit I at the end of the scalar
	proton path suggests a hydroperoxo species as the two electron reduced
	intermediate in the O-2 reduction process.},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{Yosh98,
  author = {Yoshikawa, S. and Shinzawaitoh, K. and Nakashima, R. and Yaono, R.
	and Yamashita, E. and Inoue, N. and Yao, M. and Fei, M. J. and Libeu,
	C. P. and Mizushima, T. and Yamaguchi, H. and Tomizaki, T. and Tsukihara,
	T.},
  title = {Redox-coupled crystal structural changes in bovine heart cytochrome
	c oxidase},
  journal = SCI,
  year = {1998},
  volume = {280},
  pages = {1723},
  abstract = {Crystal structures of bovine heart cytochrome c oxidase in the fully
	oxidized, fully reduced, azide-bound, and carbon monoxide-bound states
	were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution,
	respectively. An aspartate residue apart from the O-2 reduction site
	exchanges its effective accessibility to the matrix aqueous phase
	for one to the cytosolic phase concomitantly with a significant decrease
	in the pK of its carboxyl group, on reduction of the metal sites.
	The movement indicates the aspartate as the proton pumping site.
	A tyrosine acidified by a covalently linked imidazole nitrogen is
	a possible proton donor for the O-2 reduction by the enzyme.},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{YoJB98,
  author = {M.~A.~Young and B.~Jayaram and D.~L.~Beveridge},
  title = {Local dielectric environment of {B-DNA} in solution: Results from
	a 14 $ns$ molecular dynamics trajectory},
  journal = JPCB,
  year = {1998},
  volume = {102},
  pages = {7666-7669}
}

@ARTICLE{YUAN98,
  author = {Chunbo Yuan and Pamela Colb and Vincent Moy},
  title = {Viscoelastic properties of ligand-resceptor complexes},
  journal = NAT,
  year = {1998},
  note = {Submitted}
}

@ARTICLE{ZaSc98,
  author = {L.~Y. Zaslavsky and T.~Schlick},
  title = {An adaptive multigrid technique for evaluating long-range forces
	in biomolecular simulations},
  journal = AMC,
  year = {1998},
  volume = {97},
  pages = {237--250}
}

@BOOK{ZELL98,
  title = {Topologieerhaltende Neuronale Netzwerke in der Robotik},
  publisher = {Pro Universitate Verlag GmbH},
  year = {1998},
  author = {Michael Zeller},
  series = {Reihe Robotik},
  address = {Sinzheim},
  note = {ISBN 3-932490-34-7}
}

@ARTICLE{ZHAN98A,
  author = {J.-P. Zhang and C._H. Chen and Y. Koyama and H. Nagae},
  title = {Vibrational Relaxation nd redistribution in the 2{A}$_g^-$ state
	of {\em all-trans}-lycopene as revealed by picosecond time-resolved
	absorption spectroscopy},
  journal = {J.~Phys.~Chem.~B},
  year = {1998},
  volume = {102},
  pages = {1632--1640}
}

@ARTICLE{ZHAN98,
  author = {Z. Zhang and L. Huang and Y.-I. Chi and K. K. Kim and A. R. Crofts
	and E. A. Berry and S.-H. Kim},
  title = {Electron Transfer By Domain Movement in Cytochrome $bc_1$},
  journal = NAT,
  year = {1998},
  volume = {392},
  pages = {677--684},
  annote = {bc1 chicken structure}
}

@ARTICLE{Zhou98,
  author = {H.-X. Zhou},
  title = {Comparison of Three {B}rownian-Dynamics Algorithms for Calculating
	Rate Constants of Diffusion-Influenced Reactions},
  journal = {J. Chem.\ Phys.},
  year = {1998},
  volume = {108},
  pages = {8139--8145},
  number = {19}
}

@ARTICLE{ZWMC98,
  author = {H. Zhou and S.~T. Wlodek and J.~A. McCammon},
  title = {Conformation gating as a mechanism for enzyme specificity},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1998},
  volume = {95},
  pages = {9280--9283},
  note = {Biophysics}
}

@INPROCEEDINGS{BeLo97,
  author = {D. M. Beazley and P. S. Lomdahl},
  title = {Feeding a Large-Scale Physics Application to {P}ython},
  booktitle = {Proceedings of the 6th International Python conference},
  year = {1997},
  pages = {21--28},
  address = {San Jose, CA},
  month = OCT
}

@MISC{OpenMP,
  author = {Open{MP}-forum},
  title = {Open{MP}: A proposed industry standard {API} for shared memory programming.
	Technical report},
  howpublished = {{\small \texttt{http://www.openmp.org}}},
  month = OCT,
  year = {1997}
}

@INPROCEEDINGS{JaMe97a,
  author = {Du{\v s}anka Jane\v{z}i\v{c} and Franci Merzel},
  title = {An Efficient Split Integration Symplectic Method for Molecular Dynamics
	Simulations of Complex Systems},
  booktitle = {15th {IMACS} World Congress on Scientific Computation, Modelling
	and Applied Mathematics},
  year = {1997},
  editor = {Achim Sydow},
  volume = {1},
  pages = {493--498},
  address = {Berlin},
  month = AUG,
  publisher = {Wissenschaft \& Technik Verlag}
}

@INPROCEEDINGS{KALE97,
  author = {L. V. Kal{\'e} and Milind Bhandarkar and Robert Brunner and N. Krawetz
	and J. Phillips and A. Shinozaki},
  title = {{NAMD}: A Case Study in Multilingual Parallel Programming},
  booktitle = {Proc. 10th International Workshop on Languages and Compilers for
	Parallel Computing},
  year = {1997},
  pages = {367--381},
  address = {Minneapolis, Minnesota},
  month = AUG,
  institution = {Department of Computer Science and Theoretical Biophysics Group,
	Beckman Institute, University of Illinois at Urbana-Champaign}
}

@INPROCEEDINGS{BeLo97c,
  author = {D. M. Beazley and P. S. Lomdahl},
  title = {Extensible Message Passing Application Development and Debugging
	with Python},
  booktitle = {Proceeding of the 11th International Parallel Processing Symposium},
  year = {1997},
  address = {Geneva, Switzerland},
  month = APR
}

@PHDTHESIS{Aman97,
  author = {S. Amann},
  title = {Komponentenorientierte Enwicklung von Grafikapplikationen mit {BOOGA}},
  school = {Institute of Computer Science and Applied Mathematics, University
	of Berne},
  year = {1997}
}

@INPROCEEDINGS{AmSB97,
  author = {S. Amann and C. Streit and H. Bieri},
  title = {{BOOGA} -- {A} Component-Oriented Framework for Computer Grahics},
  booktitle = {GraphiCon},
  year = {1997},
  pages = {193--200},
  address = {Moscow}
}

@ARTICLE{ANST97,
  author = {G. M. Anstead and K. E. Carlson and J. A. Katzenellenbogen},
  title = {The Estradiol Pharmacophore: Ligand Structure -- Estrogen Receptor
	Binding Affinity Relationships and a Model for the Receptor Binding.},
  journal = {Steroids},
  year = {1997},
  volume = {62},
  pages = {268--303},
  annote = {review paper}
}

@CONFERENCE{AnGo97,
  author = {M. Antoniotti and A. Gollu},
  title = {{S}{H}{I}{F}{T} and {S}{M}{A}{R}{T}-{A}{H}{S}: A language for hybrid
	system engineering, modeling and simulation},
  booktitle = {Proceedings of USENIX Conference on Domain-Specific Languages},
  year = {1997},
  publisher = {Santa Barbara, CA}
}

@INPROCEEDINGS{petsc-efficient,
  author = {Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry
	F. Smith},
  title = {Efficient Management of Parallelism in Object Oriented Numerical
	Software Libraries},
  booktitle = {Modern Software Tools in Scientific Computing},
  year = {1997},
  editor = {E. Arge and A. M. Bruaset and H. P. Langtangen},
  pages = {163--202},
  publisher = {Birkhauser Press}
}

@ARTICLE{BALS97,
  author = {Manel Balsera and Sergey Stepaniants and Sergei Izrailev and Yoshitsugu
	Oono and Klaus Schulten},
  title = {Reconstructing Potential Energy Functions from Simulated Force-Induced
	Unbinding Processes},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {1281--1287}
}

@ARTICLE{BaLF97,
  author = {Bardi, Jason and Luque, Irene and Freire, Ernesto},
  title = {Structure-Based Thermodynamic Analysis of {HIV}-1 Protease Inhibitors},
  journal = BCH,
  year = {1997},
  volume = {36},
  pages = {6588--6596}
}

@ARTICLE{BARS97,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten},
  title = {Theory of Heterogeneous Relaxation in Compartmentalized Tissues},
  journal = MRM,
  year = {1997},
  volume = {37},
  pages = {666--675}
}

@ARTICLE{BaKa97,
  author = {Christian Bartels and Martin Karplus},
  title = {Multidimensional Adaptive Umbrella Sampling: Applications to Main
	Chain and Side Chain Peptide Conformations},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {1450--1462},
  number = {12}
}

@ARTICLE{BeLo97b,
  author = {D. M. Beazley and P. S. Lomdahl},
  title = {Controlling the Data Glut in Large-Scale Molecular-Dynamics Simulations},
  journal = {Computer In Physics},
  year = {1997},
  volume = {11},
  number = {3}
}

@ARTICLE{BeGO97,
  author = {Scott A. Beeser and David P. Goldenberg and Terrence G. Oas},
  title = {Enhanced Protein Flexibility Caused by a Destabilizing Amino Acid
	Replacement in BPTI},
  journal = JMB,
  year = {1997},
  volume = {269},
  pages = {154--164}
}

@ARTICLE{BKLZ97,
  author = {A. Bell and L. Kittler and G. Lober and C. Zimmer},
  title = {{DNA} binding properties of minor groove binders and influence on
	the topoisomerase {II} cleavage reaction.},
  journal = {J. Mol. Recognit.},
  year = {1997},
  volume = {10},
  pages = {245--55},
  number = {6}
}

@ARTICLE{BERG97,
  author = {Oliver Berger and Olle Edholm and Fritz J{\"a}hnig},
  title = {Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine
	at full hydration, constant pressure, and constant temperature},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {2002--2013},
  annote = {Describes lipid parameters that almost all the GROMOS people refererence.
	Also claims that surface tension doesn't matter.}
}

@ARTICLE{BERM97,
  author = {H.~M.~Berman},
  title = {Crystal studies of {B-DNA}: The answers and the questions.},
  journal = {Biopolymers},
  year = {1997},
  volume = {44},
  pages = {23--44}
}

@ARTICLE{BeSt97,
  author = {Bruce J. Berne and John E. Straub},
  title = {Novel methods of sampling phase space in the simulation of biological
	systems},
  journal = COSB,
  year = {1997},
  volume = {7},
  pages = {181--189}
}

@ARTICLE{BiSS97,
  author = {T. Bishop and R.~D. Skeel and K. Schulten},
  title = {Difficulties with Multiple Timestepping and the Fast Multipole Algorithm
	in Molecular Dynamics},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {1785--1791},
  number = {14},
  nack = {nsf96, nsfgc, nih}
}

@ARTICLE{BiKS97,
  author = {T. C. Bishop and D. Kosztin and K. Schulten},
  title = {How Hormone Receptor--{DNA} Binding Affects Nucleosomal {DNA}: The
	Role of Symmetry},
  journal = {Biophys.\ J.},
  year = {1997},
  volume = {72},
  pages = {2056--2067}
}

@ARTICLE{BISH97,
  author = {Tom Connor Bishop and Dorina Kosztin and Klaus Schulten},
  title = {How Hormone Receptor--{DNA} Binding Affects Nucleosomal {DNA}: The
	Role of Symmetry},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {2056--2067}
}

@ARTICLE{BISH97A,
  author = {T.~C. Bishop and R.~D. Skeel and K. Schulten},
  title = {Difficulties with Multiple Time Stepping and the Fast Multipole Algorithm
	in Molecular Dynamics},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {1785--1791}
}

@BOOK{SlUG97,
  title = {{ScaLAPACK} Users' Guide},
  publisher = {Society for Industrial and Applied Mathematics},
  year = {1997},
  author = {Blackford, L. S. and Choi, J. and Cleary, A. and D'Azevedo, E. and
	Demmel, J. and Dhillon, I. and Dongarra, J. and Hammarling, S. and
	Henry, G. and Petitet, A. and Stanley, K. and Walker, D. and Whaley,
	R. C.},
  address = {Philadelphia, PA},
  isbn = {0-89871-397-8 (paperback)}
}

@ARTICLE{BLOU97,
  author = {P. Blount and M. J. Schroeder and C. Kung},
  title = {Mutations in a bacterial mechanosensitive channel change the cellular
	response to osmotic stress},
  journal = JBC,
  year = {1997},
  volume = {272},
  pages = {32150--32157}
}

@ARTICLE{BORH97,
  author = {D. W. Borhani and D. P. Rogers and J. A. Engler and C. G. Brouillette},
  title = {Crystal structure of truncated human apolipoprotein {A-I} suggests
	a lipid-bound conformation},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {12291--12296},
  number = {23}
}

@MISC{Bosa97,
  author = {Jon Bosak},
  title = {XML, JAVA, and the Futrue of the web},
  year = {1997},
  note = {http://www.oasis-open.org/\-cover/\-xmlIntro.\-html},
  organization = {Sun Microsystems}
}

@ARTICLE{BRAN97,
  author = {U. Brandt},
  title = {Proton-Translocation by Membrane-Bound {NADH}-Ubiquinone-Oxidoreductase
	(Complex {I}) Through Redox-Gated Ligand Conduction},
  journal = BBAB,
  year = {1997},
  volume = {1318},
  pages = {79--01}
}

@ARTICLE{BrMM97,
  author = {D. Brown and H. Minoux and B. Maigret},
  title = {A domain decomposition parallel processing algorithm for molecular
	dynamics simulations of systems of arbitrary connectivity},
  journal = CPC,
  year = {1997},
  volume = {103},
  pages = {170--186}
}

@ARTICLE{BROW97,
  author = {K.S. Brown},
  title = {{\em Pfiesteria:} On the molecular biology of a sea monster},
  journal = {J.\ of NIH Research},
  year = {1997},
  volume = {9},
  pages = {26--27}
}

@ARTICLE{BROW97a,
  author = {S. Brown},
  title = {Metal recognition by repeating polypeptides},
  journal = {Nature Biotechnology},
  year = {1997},
  volume = {15},
  pages = {269}
}

@CONFERENCE{Bruc97,
  author = {D. Bruce},
  title = {What makes a good domain-specific language? {A}postle and its approach
	to parallel discrete event simulation},
  booktitle = {Proceedings of the First ACM Sigplan Workshop on Domain-Specific
	Languages},
  year = {1997},
  pages = {17--35},
  publisher = {ACM Press}
}

@ARTICLE{BPDH97,
  author = {Andrzej M. Brzozowski and Ashley C. W. Pike and Zbigniew Dauter and
	Roderick E. Hubbard and Tomas Bonn and Owe Engstrom and Lars Ohman
	and Geoffrey L. Greene and Jan-{A}ke Gustafsson and Mats Carlquist},
  title = {Molecular basis of agonism and antagonism in the oestrogen receptor},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {753--758}
}

@ARTICLE{BRZO97,
  author = {A.~M.~Brzozowski and A.~C.~W.~Pike and Z.~Dauter and R.~E.~Hubbard
	and T.~Bonn and O.~Engstr{\"o}m and L.~{\"O}hman and G.~L.~Greene
	and J.~A.~Gustafsson and M.~Carlquist},
  title = {Molecular basis of agonism and antagonism in the oestrogen receptor.},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {753--758}
}

@ARTICLE{CALA97,
  author = {L. Calabresi and G. Franceschini and A. Burkybile and A. Jonas},
  title = {Activation of Lecithin Cholesterol Acyltransferase by a Disulfide-Linked
	Apolipoprotein {A-I} Dimer},
  journal = BBRC,
  year = {1997},
  volume = {232},
  pages = {345--349}
}

@ARTICLE{CARL97,
  author = {Joseph W. Carlson and Ana Jonas and Stephen G. Sligar},
  title = {Imaging and Manipulation of High-Density Lipoproteins},
  journal = BJ,
  year = {1997},
  note = {Submitted}
}

@BOOK{ActiveX,
  title = {Understanding ActiveX and OLE},
  publisher = {Microsoft Press},
  year = {1997},
  author = {D. Chappell}
}

@ARTICLE{CHEA97,
  author = {T.~E.~Cheatham and P.~A.~Kollman.},
  title = {Insight into the stabilization of {A-DNA} by specific ion association:
	spontaneous {B-DNA} to {A-DNA} transitions observed in molecular
	dynamics simulations of d({ACCCGCGGGT})$_2$ in the presence of hexaamminecobalt(III)},
  journal = {Structure},
  year = {1997},
  volume = {15},
  pages = {1297--1311}
}

@INPROCEEDINGS{CHEAT97,
  author = {T.~E. Cheatham and J.~L. Miller and T.~I. Spector and P. Cieplak
	and Peter A. Kollman},
  title = {Molecular dynamics simulations on nucleic acid systems using the
	{C}ornell et al force field and particle mesh {E}wald electrostatics},
  booktitle = {ACS Symposium Series: Molecular Modeling and Structure Determination
	of Nucleic Acids},
  year = {1997},
  pages = {1--2},
  publisher = {Am. Chem. Soc.}
}

@ARTICLE{ChCG97,
  author = {Z. M. Chen and T. Cagin and W. A. Goddard},
  title = {Fast {E}wald sums for general van der {W}aals potentials},
  journal = {J. Comp. Chem.},
  year = {1997},
  volume = {18},
  pages = {1365--1370}
}

@ARTICLE{CHEN97,
  author = {A. Cheng and A.N. {van Hoek} and M. Yeager and A.S. Verkmana and
	A.K. Mitra},
  title = {Three-dimensional organization of a human water channel},
  journal = NAT,
  year = {1997},
  volume = {387},
  pages = {627--30}
}

@ARTICLE{COGD97,
  author = {R.J. Cogdell and N.W. Isaacs and A.A. Freer and J. Arrelano and T.D.
	Howard and M.Z. Papiz and A.M. Hawthornthwaite-Lawless and S. Prince},
  title = {The structure and function of the LH2 (B800-B850) complex from the
	purple bacterium {\em Rhodopseudomonas acidophila} strain 10050},
  journal = {Progr.\ Biophys.\ molec.\ Biol.},
  year = {1997},
  volume = {68},
  pages = {1--27}
}

@ARTICLE{COLL97,
  author = {T.~N.~Collingwood and O.~Rajanayagam and M.~Adams and R.~Wagner and
	V.~Cavailles and E.~Kalkhoven and C.~Matthews and E.~Nystrom and
	K.~Stenlof and G.~Lindstedt and L.~Tisell and R.~J.~Fletterick and
	M.~G.~Parker and V.~K.~K.~Chatterjee},
  title = {A natural transactivation mutation in the thyroid hormone $\beta$
	receptor: Impaired interaction with putative transcriptional mediators.},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {248--253},
  annote = {on the web}
}

@INPROCEEDINGS{DALK97,
  author = {Andrew Dalke and Klaus Schulten},
  title = {Using {TCL} for Molecular Visualization and Analysis},
  booktitle = {Proceedings of the {P}acific {S}ymposium on {B}iocomputing '97},
  year = {1997},
  volume = {2},
  pages = {85--96}
}

@ARTICLE{DaTP97,
  author = {T. Darden and A. Toukmaji and L. Pedersen},
  title = {Long-range electrostatic effects in biomolecular simulations},
  journal = {J.\ de Chimie Physique et de Physico-Chimie Biologique},
  year = {1997},
  volume = {94},
  pages = {1346--1364},
  number = {7--8}
}

@ARTICLE{DAVI97,
  author = {R. E. Davis and S. Miller and C. Herrnstadt and S. S. Ghosh and E.Fahy
	and L. A. Shinobu and D. Galasko and L. J. Thal and M. F. Beal and
	N. Howell and W. D. {Parker~Jr.}},
  title = {Mutations in mitochondrial cytochrome c oxidase genes segregate with
	late-onset {Alzheimer} disease},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {4526--4531}
}

@ARTICLE{DELA97,
  author = {J. K. Delaney and P.~ Schmidt and G.H.~Atkinson and S.~Subraminian},
  title = {Evidence for a long-lived 13-{\it cis}-containing intermediate in
	the photocycle of the Leu93 $\rightarrow$ Ala bacteriorhodopsin mutant},
  journal = {J. Phys. Chem. B.},
  year = {1997},
  volume = {101},
  pages = {5619--5621}
}

@ARTICLE{DELR97,
  author = {Jeffrey J. Delrow and Patrick J. Heath and J. Michael Schurr},
  title = {On the origin of the temperature dependence of the supercoiling free
	energy},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2688--2701}
}

@ARTICLE{DENI97,
  author = {V.~P.~Denisov and G.~Carlstrom and K.~Venu and B.~Halle.},
  title = {Kinetics of {DNA} hydration},
  journal = JMB,
  year = {1997},
  volume = {268},
  pages = {118--136}
}

@ARTICLE{DILL97,
  author = {Ken A. Dill and H. S. Chan},
  title = {From Levinthal to pathways to funnels},
  journal = NATSB,
  year = {1997},
  volume = {4},
  pages = {10--19}
}

@ARTICLE{DOW97,
  author = {Linda K. Dow and Anita Changela and Heidi E. Hefner and Mair E. A.
	Churchill},
  title = {Oxidation of a critical methionine modulates {DNA} binding of the
	{{\em Drosophila Melanogaster}} high-mobility-group protein, {HMG-D}},
  journal = FEBS,
  year = {1997},
  volume = {414},
  pages = {514--520}
}

@ARTICLE{DUAN97,
  author = {Y.~Duan and P.~Wilkosz and M.~Crowley and J.~M.~Rosenberg.},
  title = {Molecular dynamics simulation study of {DNA} dodecamer {d(CGCGAATTCGCG)}
	in solution: conformation and hydration},
  journal = JMB,
  year = {1997},
  volume = {272},
  pages = {553--572}
}

@BOOK{Dubo97,
  title = {Object Technology for Scientific Computing},
  publisher = {Prentice Hall},
  year = {1997},
  author = {Paul F. Dubois}
}

@ARTICLE{DuJo97,
  author = {K. A. Duca and P. C. Jordan},
  title = {Ion--water and water--water interactions in a gramicidin-like channel:
	effects due to group polarizability and backbone flexibility},
  journal = {Biophys. Chem.},
  year = {1997},
  volume = {65},
  pages = {123--141}
}

@ARTICLE{DKBS97,
  author = {H. Dufner and S. M. Kast and J. Brickmann and M. Schlenkrich},
  title = {Ewald summation versus direct summation of shifted-force potentials
	for the calculation of electrostatic interactions in solids: {A}
	quantitative study},
  journal = {J. Comp. Chem.},
  year = {1997},
  volume = {18},
  pages = {660--676}
}

@ARTICLE{DuLM97,
  author = {Andreas Dullweber and Benedict Leimkuhler and Robert McLachlan},
  title = {A Symplectic Splitting Method for Rigid-Body Molecular Dynamics},
  journal = {J.~Chem.\ Phys.},
  year = {1997},
  volume = {107},
  pages = {5840},
  nremark = {{University of Cambridge}, {DAMTP 1997/NA11}, {May}, 1997, {Department
	of Applied Mathematics and Theoretical Physics, Silver Street, Cambridge,
	England CB3 9EW}end nremark}
}

@ARTICLE{EATO97,
  author = {William A. Eaton and Victor Mu$\tilde{\rm n}$oz and Peggy A. Thompson
	and Chi-Kin Chan and James Hofrichter},
  title = {Submillisecond Kinetics of Protein Folding},
  journal = COSB,
  year = {1997},
  volume = {7},
  pages = {10--14}
}

@ARTICLE{EGHT97,
  author = {M. Eichinger and H. Grubm{\"u}ller and H. Heller and P. Tavan},
  title = {{FAMUSAMM}: An Algorithm for Rapid Evaluation of Electrostatic Interactions
	in Molecular Dynamics Simulations},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {1729--1749},
  annote = {EGO: http://www.lrz-muenchen.de/~heller/ego/}
}

@ARTICLE{EICH97,
  author = {C. Eichwald and J. Walleczek},
  title = {Low-frequency-dependent effects of oscillating magnetic fields on
	radical pair recombination in enzyme kinetics},
  journal = JCP,
  year = {1997},
  volume = {107},
  pages = {4943--4950}
}

@ARTICLE{ELST97,
  author = {Timothy Elston and Hongyun Wang and George Oster},
  title = {Energy Transduction in {ATP} synthase},
  journal = NAT,
  year = {1997},
  volume = {391},
  pages = {510--513},
  annote = {ATPase motor}
}

@ARTICLE{ERIC97,
  author = {Harold Erickson},
  title = {Stretching single protein modules: titin is a weird spring},
  journal = SCI,
  year = {1997},
  volume = {276},
  pages = {1090--1093}
}

@BOOK{ErNi97,
  title = {Theoretical and computational methods in genome research},
  publisher = {Plenum Press},
  year = {1997},
  editor = {Suhai},
  author = {Mats Eriksson and Lennart Nilsson},
  number = {279--286},
  address = {New York}
}

@ARTICLE{EVAN97,
  author = {Evan Evans and Ken Ritchie},
  title = {Dynamic Strength of Molecular Adhesion Bonds},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {1541--1555},
  number = {4},
  annote = {Cell adhesion. Has a review of various AFM experiments.}
}

@BOOK{FALK97,
  title = {Aquatic photosynthesis},
  publisher = {Blackwell},
  year = {1997},
  author = {P.G. Falkowski and J.A. Raven},
  address = {Malden}
}

@ARTICLE{FARS97,
  author = {R. Farshoosh and V. Chynwat and R. Gebhard and J. Lugtenburg and
	H.A. Frank},
  title = {Triplet energy transfer between the primary donor and carotenoids
	in {\em Rhodobacter sphaeroides} R-26.1 reaction center incorporated
	with spheroidene analogs having different extent of $\pi$-electron
	conjugation},
  journal = {Photochem.~Photobiol.},
  year = {1997},
  volume = {66},
  pages = {97--104}
}

@ARTICLE{FELL97A,
  author = {Scott E. Feller and Richard M. Venable and Richard W. Pastor},
  title = {Computer Simulation of a {DPPC} phospholipid bilayer: structural
	changes as a function of molecular surface area},
  journal = {Langmuir},
  year = {1997},
  volume = {13},
  pages = {6555--6561}
}

@ARTICLE{FELL97,
  author = {S. E. Feller and D. Yin and R. W. Pastor and A. D. {MacKerell Jr.}},
  title = {Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
	{P}arametrization and Comparison with Diffraction Studies},
  journal = bj,
  year = {1997},
  volume = {73},
  pages = {2269--2279},
  number = {5},
  annote = {To cite CHARMM22 field for ALKENES, cite this paper}
}

@ARTICLE{FLZB97,
  author = {Fransisco Figueirido and Ronald M. Levy and Ruhong Zhou and Bruce
	J. Berne},
  title = {Large Scale Simulation of Macromolecules in Solution: Combining the
	Periodic Fast Multipole Method with Multiple Time Step Integrators},
  journal = {J. Chem.\ Phys.},
  year = {1997},
  volume = {106},
  pages = {9835--9849},
  number = {23}
}

@ARTICLE{FITT97,
  author = {J.~Fitter and R.E.~Lechner and N.A.~Dencher},
  title = {Picosecond Molecular Motions in Bacteriorhodopsin from Neutron Scattering},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2126--2137}
}

@ARTICLE{FLEM97,
  author = {G. R. Fleming and R. {van Grondelle}},
  title = {Femtosecond spectroscopy of photosynthetic light-harvesting systems},
  journal = COSB,
  year = {1997},
  volume = {7},
  pages = {738--48}
}

@MISC{FOXT,
  author = {Fox},
  title = {Fox Toolkit},
  year = {1997},
  note = {\url{http://www.fox-toolkit.org}}
}

@ARTICLE{FRAN97,
  author = {H.A. Frank and V. Chynwat and R.Z.B. Desamero and R. Farshoosh and
	J. Erickson and J. Bautista},
  title = {On the photophysics and photochemical properties of carotenoids and
	their role as light-harvesting pigments in photosynthesis},
  journal = PAC,
  year = {1997},
  volume = {68},
  pages = {2117--2124}
}

@ARTICLE{FRAN97A,
  author = {H.A. Frank and R.Z.B. Desamero, V. Chynwat and R. Gebhard and I.
	van der Hoef and F.J. Jansen and J. Lugtenburg and D. Gosztola and
	M.R. Wasielewski},
  title = {Spectroscopic Properties of Spheroidene Analogs Having Different
	Extents of $\pi$-Electron Conjugation},
  journal = JPCA,
  year = {1997},
  volume = {101},
  pages = {149--157}
}

@ARTICLE{GALL97,
  author = {A. Gall and G. J. S. Fowler and C. N. Hunter and B. Robert},
  title = {Influence of the Protein Binding Site on the Absorption Properties
	of the Monomeric Bacteriochlorophyll in {\em {R}hodobacter sphaeroides}
	{LH}2 Complex},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {16282--16287}
}

@ARTICLE{GILS97,
  author = {M.K. Gilson and J.A. Given and B.L. Bush and J.A. McCammon},
  title = {The Statistical-Thermodynamic Basis for Computation of Binding Affinities:
	{A} Critical Review},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {1047--1069}
}

@ARTICLE{GlSh97,
  author = {James Glimm and David H. Sharp},
  title = {Multiscale Science: A Challenge for the Twenty-First Century},
  journal = {SIAM News},
  year = {1997},
  volume = {30},
  pages = {4, 17, 19},
  number = {8}
}

@MISC{GNU97,
  author = {GNU},
  title = {GNU Automake - GNU Project - Free Software Foundation},
  howpublished = {\url{http://www.gnu.org/software/automake}},
  year = {1997},
  annote = {GNU Automake Homepage},
  readme = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{GNTB97,
  author = {J. M. Gottesfeld and L. Neely and J. W. Trauger and E. E. Baird and
	P. B. Dervan},
  title = {Regulation of gene expression by small molecules},
  journal = NAT,
  year = {1997},
  volume = {287},
  pages = {202--205}
}

@ARTICLE{GRAN97,
  author = {H. Granzier and M. Kellermayer and M. Helmes and K. Trombitas},
  title = {Titin elasticity and mechanism of passive force development in rat
	cardiac myocytes probed by thin-film extraction},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2043--2053}
}

@ARTICLE{GrRo97,
  author = {L. Greengard and V. Rokhlin},
  title = {A new version of the fast multipole method for the {L}aplace equation
	in three dimensions},
  journal = {Acta Numerica},
  year = {1997},
  volume = {6},
  pages = {229--269}
}

@ARTICLE{GrWa97,
  author = {Robert D. Groot and Patrick B. Warren},
  title = {Dissipative Particle Dynamics: Bridging the Gap Between Atomistic
	and Mesoscopic Simulation},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {4423--4435},
  number = {11}
}

@ARTICLE{Hair97,
  author = {E. Hairer},
  title = {Variable Time Step Integration with Symplectic Methods},
  journal = {Appl.\ Numer.\ Math.},
  year = {1997},
  volume = {25},
  pages = {219--227},
  number = {2--3}
}

@ARTICLE{HaLu97,
  author = {Ernst Hairer and Christian Lubich},
  title = {The Life-span of Backward Error Analysis for Numerical Integrators},
  journal = {Numer.\ Math.},
  year = {1997},
  volume = {76},
  pages = {441--462}
}

@ARTICLE{Hans97,
  author = {Ulrich H.E. Hansmann},
  title = {Parallel tempering algorithm for conformational studies of biological
	molecules},
  journal = CPL,
  year = {1997},
  volume = {281},
  pages = {140--150}
}

@MASTERSTHESIS{Hard97,
  author = {David J. Hardy},
  title = {Multiple Time Step Symplectic Integration},
  school = {University of Missouri--Rolla},
  year = {1997}
}

@ARTICLE{HENN97,
  author = {U. Henningsen and M. Schliwa},
  title = {Reversal in the direction of movement of a molecular motor},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {93--95}
}

@ARTICLE{HiCa97,
  author = {M. L. Hines and N. T. Carnevale},
  title = {The {N}{E}{U}{R}{O}{N} simulation environment},
  journal = {Neural Computation},
  year = {1997},
  volume = {9},
  pages = {1179--1209},
  number = {6}
}

@ARTICLE{HIRO97,
  author = {K. Hirose and W.B. Amos and A. Lockhart and R.A. Cross and L.A. Amos},
  title = {Three-dimensional cryoelectron microscopy of 16-protofilament microtubules:
	Structure, polarity, and interaction with motor proteins},
  journal = JSB,
  year = {1997},
  volume = {118},
  pages = {140--148}
}

@ARTICLE{HOEN97,
  author = {A. Hoenger and R.A. Milligan},
  title = {Motor domains of kinesin and ncd interact with microtubule protofilaments
	with the same binding geometry},
  journal = JMB,
  year = {1997},
  volume = {265},
  pages = {553--564}
}

@ARTICLE{HOWA97,
  author = {Joe Howard},
  title = {Molecular motors: Structural Adaptations to Cellular Functions},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {561--567}
}

@ARTICLE{HU97C,
  author = {J. G. Hu and B. Q. Sun and A. T. Petkova and R. G. Griffin and J.
	H. Herzfeld},
  title = {The Predischarge Chromophore in Bacteriorhodopsin: A 15-N Solid-State
	{NMR} Study of the L Photointermediate},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {9316--9322}
}

@ARTICLE{HU97,
  author = {Xiche Hu and Thorsten Ritz and Ana Damjanovi\'c and Klaus Schulten},
  title = {Pigment Organization and Transfer of Electronic Excitation in the
	Purple Bacteria},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {3854--3871}
}

@ARTICLE{HU97B,
  author = {Xiche Hu and Klaus Schulten},
  title = {How Nature Harvests Sunlight},
  journal = {Physics Today},
  year = {1997},
  volume = {50},
  pages = {28--34}
}

@ARTICLE{HuLe97,
  author = {W. Huang and B. Leimkuhler},
  title = {The Adaptive {V}erlet Method},
  journal = SJSC,
  year = {1997},
  volume = {18},
  pages = {239--256}
}

@ARTICLE{HUBE97,
  author = {G.A. Huber and J.A. McCammon},
  title = {Weighted-ensemble simulated annealing: Faster optimization on hierarchical
	energy surfaces},
  journal = PRE,
  year = {1997},
  volume = {55},
  pages = {4822--4825}
}

@ARTICLE{HUMP97,
  author = {William Humphrey and Ernst Bamberg and Klaus Schulten},
  title = {Photoproducts of Bacteriorhodopsin Mutants: A Molecular Dynamics
	Study},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {1347--1356}
}

@ARTICLE{ISRA97,
  author = {B. Isralewitz and S. Izrailev and K. Schulten},
  title = {Binding Pathway of Retinal to Bacterio-opsin: {A} Prediction by Molecular
	Dynamics Simulations},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2972--2979}
}

@INPROCEEDINGS{Izag97,
  author = {J.~A. Izaguirre},
  title = {Empirical Evaluation of Graph Partitioning Algorithms},
  booktitle = {Proceedings of the National Computer Science Encounter},
  year = {1997},
  pages = {44--50},
  address = {M\'exico},
  organization = {Sociedad Nacional de Computaci\'on},
  note = {Preprint: \url{http://www.nd.edu/~izaguirr/papers/enc97.pdf}}
}

@ARTICLE{IZRA97,
  author = {Sergei Izrailev and Sergey Stepaniants and Manel Balsera and Yoshi
	Oono and Klaus Schulten},
  title = {Molecular Dynamics Study of Unbinding of the Avidin-Biotin Complex},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {1568--1581}
}

@ARTICLE{JaMe97b,
  author = {Du{\v s}anka Jane\v{z}i\v{c} and Franci Merzel},
  title = {Split Integration Symplectic Method for Molecular Dynamics Integration},
  journal = {J. Chem.\ Inf.\ Comput.\ Sci.},
  year = {1997},
  volume = {37},
  pages = {1048--1054},
  number = {6}
}

@ARTICLE{JARZ97,
  author = {C. Jarzynski},
  title = {Nonequilibrium Equality for Free Energy Differences},
  journal = PRL,
  year = {1997},
  volume = {78},
  pages = {2690--2693}
}

@ARTICLE{JARZ97a,
  author = {C. Jarzynski},
  title = {Equilibrium Free-Energy Differences from Nonequilibrium Measurements:
	{A} Master Equation Approach},
  journal = PRE,
  year = {1997},
  volume = {56},
  pages = {5018--5035}
}

@ARTICLE{JIME97,
  author = {R. Jimenez and F. {van Mourik} and J. Y. Yu and G. R. Fleming},
  title = {Three-Pulse Photon Echo Measurements on LH1 and LH2 Complexes of
	{\em Rhpdpbacter sphaeroides}: A Nonlinear Spectroscopic Probe of
	Energy Transfer},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {7350--7359}
}

@ARTICLE{JUNG97,
  author = {Wolfgang Junge and Holger Lill and Siegfried Engelbrecht},
  title = {ATP synthase: an electrochemical transducer with rotary mechanics},
  journal = TIBS,
  year = {1997},
  volume = {22},
  pages = {420--423}
}

@ARTICLE{JUZE97,
  author = {G. Juzeliunas and P. Reineker},
  title = {Influence of exciton-exciton interaction on one-to-two exciton transitions
	in molecular aggregates with linear and circular geometries},
  journal = JCP,
  year = {1997},
  volume = {107},
  pages = {9801--9806}
}

@ARTICLE{KBCH97,
  author = {K. Karplus and C. Barrett and M. Cline and D. Haussler and R. Hughey
	and L. Holm and C. Sander},
  title = {Predicting Protein Structure Using Hidden Markov Models},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1997},
  volume = {29S},
  pages = {134--139}
}

@ARTICLE{KELL97,
  author = {M. Kellermayer and S. Smith and H. Granzier and C. Bustamante},
  title = {Folding-Unfolding Transition in Single Titin Modules Characterized
	With Laser Tweezers},
  journal = SCI,
  year = {1997},
  volume = {276},
  pages = {1112--1116}
}

@ARTICLE{KENN97,
  author = {J. T. M. Kennis and A. M. Streltsov and H. Permentier and T. J. Aartsma
	and J. Amesz},
  title = {Exciton Coherence and Energy Transfer in the {LH2} Antenna Complex
	of {\em {R}hodopseudomonas acidophila} at Low Temperature},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {8369--8374}
}

@ARTICLE{KERS97,
  author = {S.~Kersten and P.~R.~Reczek and N.~Noy.},
  title = {The tetramerization region of the retinoid X receptor is important
	for transcriptional activation by the receptor},
  journal = JBC,
  year = {1997},
  volume = {272},
  pages = {29759--29768}
}

@ARTICLE{KIMU97,
  author = {Y.~Kimura and D.~G.~Vassylyev and E.~Miyazawa and A.~Kidera and M.~Matsushima
	and K.~Mitsuoka and K.~Murata and T.~Hirai and Y.~Fujiyoshi},
  title = {Surface of Bacteriorhodopsin Revealed by High-Resolution Electron
	Crystallography},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {206--211}
}

@ARTICLE{KNOX97,
  author = {R.S. Knox},
  title = {Excitons and their equilibration},
  journal = {Pure \& Appl.~Chem.},
  year = {1997},
  volume = {69},
  pages = {1163--1170}
}

@BOOK{Knut97,
  title = {Art of Computer Programming, Volume 2: Seminumerical Algorithms},
  publisher = {Addison-Wesley},
  year = {1997},
  author = {Donald E. Knuth},
  address = {Reading, Massachusetts},
  edition = {3rd}
}

@ARTICLE{KoLL97,
  author = {A. Kol and B. Laird and B. Leimkuhler},
  title = {A symplectic method for rigid-body molecular simulation},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {2580--2588},
  number = {7}
}

@ARTICLE{KoBS97,
  author = {Dorina Kosztin and Thomas C. Bishop and Klaus Schulten},
  title = {Binding of the Estrogen Receptor to {DNA}: {T}he Role of Waters},
  journal = {Biophys.\ J.},
  year = {1997},
  volume = {73},
  pages = {557--570}
}

@ARTICLE{KOSZ97A,
  author = {Dorina Kosztin and Thomas C. Bishop and Klaus Schulten},
  title = {Binding of the Estrogen Receptor to {DNA}: {T}he Role of Waters},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {557--570}
}

@ARTICLE{KOSZ97,
  author = {Ioan Kosztin and Klaus Schulten},
  title = {Boundary Integral Method for Stationary States of Two-Dimensional
	Quantum Systems},
  journal = IJMPC,
  year = {1997},
  volume = {8},
  pages = {293--325}
}

@ARTICLE{LABE97,
  author = {S. Labeit and B. Kolmerer and W. Linke},
  title = {The giant protein titin: emerging roles in physiology and pathophysiology},
  journal = CIR,
  year = {1997},
  volume = {80},
  pages = {290--294}
}

@ARTICLE{LANC97,
  author = {C. R. Lancaster and H. Michel},
  title = {The Coupling of Light-Induced Electron Transfer and Proton Uptake
	as Derived from Crystal Structures of Reaction Centers from {\em
	{R}hodopseudomonas viridis} Modified at the Binding Site of the Secondary
	Quinone, {QB}},
  journal = STR,
  year = {1997},
  volume = {5},
  pages = {1339--1359}
}

@ARTICLE{LAZA97,
  author = {T Lazaridis and M Karplus},
  title = {New view of protein folding reconciled with the old through multiple
	unfolding simulations},
  journal = SCI,
  year = {1997},
  volume = {278},
  pages = {1928--1931}
}

@INCOLLECTION{LeDL97,
  author = {M. H. Lee and M. J. Duncan and H. F. Levison},
  title = {Variable Timestep Integrators for Long-Term Orbital Integrations},
  booktitle = {Computational Astrophysics, Proc. 12th Kingston Meeting},
  year = {1997}
}

@ARTICLE{Levi97,
  author = {M. Levitt},
  title = {Competitive Assessment of Protein Fold Recognition and Threading
	Accuracy},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1997},
  volume = {29S},
  pages = {92--104}
}

@ARTICLE{LGHT97,
  author = {M. Levitt and E. S. Gerstein and S. S. Huang and J. Tsai},
  title = {Protein Folding: The End-Game},
  journal = {Ann. Rev. Biochemistry},
  year = {1997},
  volume = {66},
  pages = {549--579}
}

@ARTICLE{LHSL97,
  author = {M. Levitt and M. Hirshberg and R. Sharon and K. E. Laidig and V.
	Daggett},
  title = {Calibration and Testing of a Water Model for Simulation of the Molecular
	Dynamics of Proteins and Nucleic Acids in Solution},
  journal = {J. Phys. Chem.},
  year = {1997},
  volume = {B25},
  pages = {5051--5061}
}

@ARTICLE{LIM97,
  author = {K.-T. Lim and S. Brunett and M. Iotov and R.B. McClurg and N. Vaidehi
	and S. Dasgupta and S. Taylor and W.A. {Goddard III}},
  title = {Molecular dynamics for very large systems on massively parallel computers:
	The {MPS}im program},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {501--521}
}

@ARTICLE{LiSZ97,
  author = {T.R. Littell and R.D. Skeel and M. Zhang},
  title = {Error Analysis of Symplectic Multiple Time Stepping},
  journal = SJNA,
  year = {1997},
  volume = {34},
  pages = {1792--1807},
  number = {5}
}

@BOOK{LOUD97,
  title = {Compiler Construction: Principles and Practice},
  publisher = {PWS Publishing Company},
  year = {1997},
  author = {K. C. Louden},
  address = {Cincinnati}
}

@ARTICLE{LOWA97,
  author = {P.~T.~Lowary and J.~Widom},
  title = {Short-range Order in Two Eukaryotic Genomes: Relation to Chromosome
	Structure},
  journal = PNAS,
  year = {1997},
  note = {In press}
}

@ARTICLE{LUGE97,
  author = {Karolin Luger and Armin W. M{\"a}der and Robin K. Richmond and David
	F. Sargent and Timothy J. Richmond},
  title = {Crystal structure of the nucleosome core particle at {2.8\,\AA} resolution},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {251--260}
}

@ARTICLE{LUED97,
  author = {Susanna K. L{\"u}demann and Oliviero Carugo and Rebecca C. Wade},
  title = {Substrate Access to Cytochrome {P450cam}: A Comparison of a Thermal
	Motion Pathway Analysis with Molecular Dynamics Simulation Data},
  journal = JMM,
  year = {1997},
  volume = {3},
  pages = {369--374}
}

@ARTICLE{LoSS97,
  author = {M. L{\'o}pez-Marcos and J. M. Sanz-Serna and R.~D. Skeel},
  title = {Explicit Symplectic Integrators Using {H}essian--Vector Products},
  journal = SJSC,
  year = {1997},
  volume = {18},
  pages = {223--238},
  nack = {Iber, doensf, nsfarpa, nih}
}

@ARTICLE{MA97B,
  author = {J.~Ma and M.~Karplus},
  title = {{Molecular switch in signal transduction: Reaction paths of the conformational
	changes in {\em ras} p21}},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {11905--11910}
}

@ARTICLE{MA97A,
  author = {Y.Z. Ma and R.J. Cogdell and T. Gillbro},
  title = {Energy transfer and exciton annihilation in the B800-850 antenna
	complex of the photosynthetic purple bacterium {\em Rhodopseudomonas
	acidophila} (strain 10050) - a femtosecond transient absorption study},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {1087--1095}
}

@ARTICLE{MA97,
  author = {Y.-Z. Ma and E. W. Taylor},
  title = {Interacting head mechanism of microtubule-kinesin {ATP}ase},
  journal = JBC,
  year = {1997},
  volume = {272},
  pages = {724--730}
}

@ARTICLE{MARR97,
  author = {T.J. Marrone and J.M. Briggs and J.A. McCammon},
  title = {Structure-Based Drug Design: {C}omputational Advances},
  journal = ARPT,
  year = {1997},
  volume = {37},
  pages = {71--90}
}

@ARTICLE{MaBE97,
  author = {C. A. Marsh and G. Backx and M. H. Ernst},
  title = {Static and Dynamic Properties of Dissipative Particle Dynamics},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {56},
  pages = {1676--1691},
  number = {2}
}

@ARTICLE{MART97,
  author = {E.~Martinez and D.~D.~Moore and E.~Keller and D.~Pearce and V.~Robinson
	and P.~Macdonald and S.~S.~Simons and E.~Sanchez and M.~Danielsen.},
  title = {The nuclear receptor resource project},
  journal = NAR,
  year = {1997},
  volume = {25},
  pages = {163--165}
}

@ARTICLE{MART97A,
  author = {T. J.~Mart{\'{\i}}nez and M.~Ben-Nun and R. D.~Levine},
  title = {Molecular Collision Dynamics on Several Electronic States},
  journal = JPCA,
  year = {1997},
  volume = {101},
  pages = {6389}
}

@ARTICLE{MART97B,
  author = {Mart{\'{\i}}nez, T J and Levine, R D},
  title = {Non-adiabatic Molecular Dynamics: Split Operator Multiple Spawning
	with Applications to Photodissociation},
  journal = {J. Chem. Soc.: Faraday Transactions},
  year = {1997},
  volume = {93},
  pages = {940--947}
}

@ARTICLE{MARU97,
  author = {K. Maruyama},
  title = {Connectin/titin, a giant elastic protein of muscle},
  journal = FASEB,
  year = {1997},
  volume = {11},
  pages = {341--345}
}

@MASTERSTHESIS{Matt97,
  author = {T. Matthey},
  title = {Objektorientierte {G}eb{\"a}udemodellierung},
  school = {Institute of Computer Science and Applied Mathematics, University
	of Berne},
  year = {1997}
}

@ARTICLE{Mazu97,
  author = {Alexey K. Mazur},
  title = {Common Molecular Dynamics Algorithms Revisited: Accuracy and Optimal
	Time Stpes of St\"ormer--Leapfrog},
  journal = {J. Comput.\ Phys.},
  year = {1997},
  volume = {136},
  pages = {354--365},
  nremark = {530.1505 JOR PHX}
}

@ARTICLE{McGr98,
  author = {Robert I. McLachlan and Stephen K. Gray},
  title = {Optimal Stability Polynomials for Splitting Methods, With Application
	to the Time-Dependent {S}chr\"odinger Equation},
  journal = {Appl.\ Numer.\ Math.},
  year = {1997},
  volume = {25},
  pages = {275--286},
  number = {2--3}
}

@ARTICLE{MEIE97,
  author = {T. Meier and Y. Zhao and V. Chernyak and S. Mukamel},
  title = {Polarons, Localization, and Excitonic Coherence in Superradiance
	of Biological Antenna Complexes},
  journal = JCP,
  year = {1997},
  volume = {107},
  pages = {3876--3893},
  number = {10}
}

@ARTICLE{MeBa97,
  author = {E. Merritt and D. Bacon},
  title = {Raster3D: Photorealistic molecular graphics},
  journal = ME,
  year = {1997},
  volume = {277},
  pages = {505--524}
}

@BOOK{Meye97,
  title = {Object-Oriented Software Construction},
  publisher = {Prentice-Hall},
  year = {1997},
  author = {B. Meyer},
  edition = {2nd}
}

@ARTICLE{MONS97,
  author = {R. Monshouwer and M. Abrahamsson and F. {van Mourik} and R. {van
	Grondelle}},
  title = {Superradiance and Exciton Delocalization in Bacterial Photosynthetic
	Light-Harvesting Systems},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {7241--7248}
}

@ARTICLE{MORI97,
  author = {H. Morii and T. Takenawa and F. Arisaka and T. Shimizu},
  title = {Identification of kinesin neck region as a stable $\alpha$-helical
	coiled coil and its thermodynamic characterization},
  journal = BCH,
  year = {1997},
  volume = {36},
  pages = {1933--1942}
}

@ARTICLE{MTHE97,
  author = {Victor Mu$\tilde{\rm n}$oz and Peggy A. Thompson and James Hofrichter
	and William A. Eaton},
  title = {Folding dynamics and mechanism of $\Beta$-hairpin formation},
  journal = NAT,
  year = {1997},
  volume = {390},
  pages = {196--199}
}

@ARTICLE{MUNO97,
  author = {V. Munoz and P. Thompson and J. Hofrichter and W. Eaton},
  title = {Folding dynamics and mechanism of beta-hairpin formation},
  journal = NAT,
  year = {1997},
  volume = {390},
  pages = {196--199}
}

@ARTICLE{MUNR97,
  author = {U. Munro and J.A. Munro and J.B. Philipps and W. Wiltschko},
  title = {Effect of wavelength of light and pulse magnetization on different
	magnetoreception systems in a migratory bird},
  journal = {Austral.~J.~Zool.},
  year = {1997},
  volume = {45},
  pages = {189--198}
}

@ARTICLE{MUNR97A,
  author = {Ursula Munro and J.A. Munro and J.B. Phillips and R. Wiltschko and
	W. Wiltschko},
  title = {Evidence for a magnetite-based navigational map in birds},
  journal = {Naturwiss.},
  year = {1997},
  volume = {84},
  pages = {26--28}
}

@ARTICLE{Neum97,
  author = {Arnold Neumaier},
  title = {Molecular modeling of proteins and mathematical prediction of protein
	structure},
  journal = {SIAM Rev.},
  year = {1997},
  volume = {39},
  pages = {407--460},
  number = {3}
}

@ARTICLE{NOJI97,
  author = {Hiroyuki Noji and Tyohei Yasuda and Masasuke Yoshida and Kazuhiko
	Kinosita Jr.},
  title = {Direct observation of the rotation of {F1}-{ATP}ase},
  journal = NAT,
  year = {1997},
  volume = {386},
  pages = {299--302}
}

@ARTICLE{ONUC97,
  author = {J. N. Onuchic and Z. Luthey-Schulten and P. G. Wolynes},
  title = {Theory of Protein Folding: The Energy Landscape Perspective},
  journal = {Annu. Rev. Phys. Chem.},
  year = {1997},
  volume = {48},
  pages = {545--600}
}

@ARTICLE{OSTE97,
  author = {Ostermeier, C. and Harrenga, A. and Ermler, U. and Michel, H.},
  title = {Structure at 2.7 \AA{} resolution of the Paracoccus denitrificans
	two-subunit cytochrome c oxidase complexed with an antibody FV fragment},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {10547},
  abstract = {The aa3 type cytochrome c oxidase consisting of the core subunits
	I and II only was isolated from the soil bacterium Paracoccus denitrificans
	and crystallized as complex with a monoclonal antibody Fv fragment.
	Crystals could be grown in the presence of a number of different
	nonionic detergents. However, only undecyl--D-maltoside and cyclohexyl-hexyl--D-maltoside
	yielded well-ordered crystals suitable for high resolution x-ray
	crystallographic studies. The crystals belong to space group P212121
	and diffract x-rays to at least 2.5 \AA{} (1 \AA{} = 0.1 nm) resolution
	using synchrotron radiation. The structure was determined to a resolution
	of 2.7 \AA{} using molecular replacement and refined to a crystallographic
	R-factor of 20.5% (Rfree = 25.9%). The refined model includes subunits
	I and II and the 2 chains of the Fv fragment, 2 heme A molecules,
	3 copper atoms, and 1 Mg/Mn atom, a new metal (Ca) binding site,
	52 tentatively identified water molecules, and 9 detergent molecules.
	Only four of the water molecules are located in the cytoplasmic half
	of cytochrome c oxidase. Most of them are near the interface of subunits
	I and II. Several waters form a hydrogen-bonded cluster, including
	the heme propionates and the Mg/Mn binding site. The Fv fragment
	binds to the periplasmic polar domain of subunit II and is critically
	involved in the formation of the crystal lattice. The crystallization
	procedure is well reproducible and will allow for the analysis of
	the structures of mechanistically interesting mutant cytochrome c
	oxidases.},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{OWEN97,
  author = {G.M. Owen and A.J. Hoff and M.R. Jones},
  title = {Excitonic interactions between the reaction center and antennae in
	purple photosynthetic bacteria},
  journal = {J.~Phys.~Chem.~B},
  year = {1997},
  volume = {101},
  pages = {7197--7204}
}

@ARTICLE{PASSN97,
  author = {J. M. Passner and T. A. Steitz},
  title = {The structure of a {CAP-DNA} complex having two {cAMP} molecules
	bound to each monomer},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {2843--2847}
}

@ARTICLE{PAVE97,
  author = {J. J. Pavelites and P. A. Bash and J. Gao and A. D. {MacKerell Jr.}},
  title = {Molecular Mechanics Force Field for {NAD+}, {NADH}, and the Pyrophosphate
	Groups of Nucleotides},
  journal = JCC,
  year = {1997},
  volume = {18},
  pages = {221--239},
  annote = {To cite CHARMM22 field for NAD(P)+, NAD(P)H, and PPI, cite this paper}
}

@ARTICLE{PEBA97,
  author = {E.~Pebay-Peyroula and G.~Rummel and J.~P.~Rosenbusch and E.~M.~Landau},
  title = {X-ray Structure of Bacteriorhodopsin at 2.5 {Angstroms} from Microcrystals
	Grown in Lipidic Cubic Phases},
  journal = SCI,
  year = {1997},
  volume = {227},
  pages = {1676--1691}
}

@ARTICLE{PeMo97,
  author = {J. T. Pedersen and J. Moult},
  title = {Folding Simulation with Genetic Algorithms and a Detailed Molecular
	Description},
  journal = {J. Mol. Biol.},
  year = {1997},
  volume = {269},
  pages = {240--259}
}

@ARTICLE{PERS97,
  author = {A. Persidis},
  title = {Catalytic Antibodies. {S}ome Companies are Taking an Active Interest
	in this Promising Technology},
  journal = {Nature Biotechnology},
  year = {1997},
  volume = {15},
  pages = {1313--1315}
}

@ARTICLE{PFUH97,
  author = {M. Pfuhl and S. Improta and A. Politou and A. Pastore},
  title = {When a module is also a domain: the role of the N terminus is the
	stability and the dynamics of immunoglobulin domains from titin},
  journal = JMB,
  year = {1997},
  volume = {265},
  pages = {242--256}
}

@ARTICLE{PHIL97,
  author = {James C. Phillips and Willy Wriggers and Zhigang Li and Ana Jonas
	and Klaus Schulten},
  title = {Predicting the structure of apolipoprotein {A-I} in reconstituted
	high density lipoprotein disks},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2337--2346}
}

@ARTICLE{RADM96,
  author = {Radmer and Kollman},
  title = {Free energy calculation methods: A theoretical and empirical comparison
	of numerical errors and a new method for qualitative estimates of
	free energy changes},
  journal = {Journal of Computational Chemistry},
  year = {1997},
  volume = {18},
  pages = {902--919},
  number = {7}
}

@PHDTHESIS{Rank97,
  author = {W. T. Rankin},
  title = {Efficient Parallel Implementations of Multipole Based N-Body Algorithms},
  school = {Duke University},
  year = {1997},
  annote = {ntroduction Multipole-based Algorithms provide O(N) or O(N log N)
	solution to computation of N-body interaction problems. These types
	of problems are seen in a wide variety of applications including
	molecular dynamics, fluid dynamics, and astrophysical simulation,
	among others. Efficient O(N) implementations can provide a significant
	time savings over other methods for medium to large sized simulations.
	Maximizing the performance of these algorithms involves improvements
	to both the base algorithms as well as an efficient parallel and
	distributed implementations. The proposed dissertation research will
	cover three major areas: 1. A distributed memory implementation of
	the Parallel...}
}

@ARTICLE{RIEF97,
  author = {Matthias Rief and Mathias Gautel and Filipp Oesterhelt and Julio
	M. Fernandez and Hermann E. Gaub},
  title = {Reversible unfolding of individual titin immunoglobulin domains by
	{A}{F}{M}},
  journal = SCI,
  year = {1997},
  volume = {276},
  pages = {1109--1112}
}

@ARTICLE{ROGE97,
  author = {Denise P. Rogers and Christie G. Brouillette and Jeffrey A. Engler
	and Susan W. Tendian and Linda Roberts and Vinod K. Mishra and G.
	M. Anantharamaiah and Sissel Lund-Katz and Michael C. Phillips and
	Marjorie J. Ray},
  title = {Truncation of the Amino Terminus of Human Apolipoprotein {A-I} Substantially
	Alters Only the Lipid-Free Conformation},
  journal = BCH,
  year = {1997},
  volume = {36},
  pages = {288--300}
}

@ARTICLE{RUVC97,
  author = {V. V. Rybenkov and C. J. Ullsperger and A. V. Vologodskii and N.
	R. Cozzarelli},
  title = {Simplification of DNA Topology Below Equilibrium Values by Type II
	Topoisomerases},
  journal = SCI,
  year = {1997},
  volume = {277},
  pages = {690--693}
}

@ARTICLE{SASA97,
  author = {T.~Sasaki and N.~Morisaki and S.~Iwasaki and H.~Kagechika and H.~Fukasawa
	and K.~Shudo and Y.~Shida and Y.~Hashimoto},
  title = {Photoaffinity labeling of the ligand-interacting helix of the retinoic
	acid receptor alpha.},
  journal = BPB,
  year = {1997},
  volume = {20},
  pages = {913--916},
  annote = {experimental stuff}
}

@ARTICLE{SaHo97,
  author = {N.~J. Savill and P.~Hogeweg},
  title = {Modelling morphogenesis: from single cells to crawling slugs},
  journal = {J. Theor. Biol.},
  year = {1997},
  volume = {184},
  pages = {229--235}
}

@ARTICLE{SFS+97,
  author = {J. Schaff and C. C. Fink and B. Slepchenko and J. H. Carson and L.
	M. Loew},
  title = {A general computational framework for modeling cellular structure
	and function},
  journal = {Biophys. J.},
  year = {1997},
  volume = {73},
  pages = {1135--1145}
}

@INCOLLECTION{ScBM97,
  author = {Tamar Schlick and Eric Barth and Margaret Mandziuk},
  title = {Biomolecular Dynamics at Long Timesteps: Bridging the Timescale Gap
	Between Simulation and Experimentation},
  booktitle = {Annual Review of Biophysics and Biomolecular Structure},
  year = {1997},
  editor = {Robert M. Stroud},
  volume = {26},
  note = {In Press}
}

@ARTICLE{ScLe97,
  author = {K. E. Schmidt and M. A. Lee},
  title = {Multipole {E}wald sums for the fast multipole method},
  journal = {J. Stat. Phys.},
  year = {1997},
  volume = {89},
  pages = {411--424}
}

@ARTICLE{SCHO97,
  author = {Gregory D. Scholes and Richard D. Harcourt and Graham R. Fleming},
  title = {Electronic Interactions in Photosynthetic Light-Harvesting Complexes:
	The Role of Carotenoids},
  journal = {J.~Phys.~Chem.~B},
  year = {1997},
  volume = {101},
  pages = {7302--7312}
}

@INCOLLECTION{SCHU97,
  author = {Klaus Schulten and Hui Lu and Linsen Bai},
  title = {Probing Protein Motion Through Temperature Echoes},
  booktitle = {Physics of Biological Systems: From Molecules to Species},
  publisher = {Springer},
  year = {1997},
  editor = {Henrik Flyvbjerg and John Hertz and Mogens H. Jensen and Ole G. Mouritsen
	and Kim Sneppen},
  series = {Lecture Notes in Physics},
  pages = {117--152}
}

@ARTICLE{SCHW97,
  author = {J.~W.~R.~Schwabe},
  title = {The role of water in protein--{DNA} interactions},
  journal = COSB,
  year = {1997},
  volume = {7},
  pages = {126--134},
  annote = {review article}
}

@ARTICLE{SIM97,
  author = {E. Sim and N. Makri},
  title = {Path integral simulation of charge transfer dynamics in photosynthetic
	reaction centers},
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {5446--5458}
}

@ARTICLE{SAJG97,
  author = {S. G. Sirnivasan and I. Ashok and H. J{\^o}nsson and G. Kalonji and
	J. Zahorjan},
  title = {Parallel short-range molecular dynamics using the {A}dhara runtime
	system},
  journal = {Computer Physics Communications},
  year = {1997},
  volume = {102},
  pages = {28--43}
}

@ARTICLE{SAJG97b,
  author = {S. G. Sirnivasan and I. Ashok and H. J{\^o}nsson and G. Kalonji and
	J. Zahorjan},
  title = {Dynamics-domain-decomposition parallel molecular dynamics},
  journal = {Computer Physics Communications},
  year = {1997},
  volume = {102},
  pages = {44--58}
}

@ARTICLE{SkZS97,
  author = {R.~D. Skeel and Guihua Zhang and Tamar Schlick},
  title = {A family of symplectic integrators: stability, accuracy, and molecular
	dynamics applications},
  journal = SJSC,
  year = {1997},
  volume = {18},
  pages = {203--222},
  number = {1},
  ack = {doe91, nsf93, gc, nih92}
}

@CONFERENCE{SmBa97,
  author = {Yannis Smaragdakis and Don Batory},
  title = {DiSTiL: A Transformation Library for Data Structures},
  booktitle = {Domain-Specific Languages Conference '97},
  year = {1997}
}

@TECHREPORT{Smit97,
  author = {L. Smith},
  title = {Molecular Science Modelling},
  institution = {Edinburgh Parallel Computing Center, The University of Edinburgh,
	UK},
  year = {1997},
  annote = {http://www.epcc.ed.ac.uk/epcc-tec/documents/}
}

@ARTICLE{SOSA97,
  author = {H. Sosa and P. Dias and A. Hoenger and M. Whittaker and E. Wilson-Kubalek
	and E. Sablin and R.J. Fletterick and R.D. Vale and R.A. Milligan},
  title = {A Model for the microtubule-ncd motor protein complex obtained by
	cryo-electron microscopy and image analysis},
  journal = CEL,
  year = {1997},
  volume = {90},
  pages = {217--224}
}

@ARTICLE{STEP97A,
  author = {Sergey Stepaniants and Sergei Izrailev and Klaus Schulten},
  title = {Extraction of Lipids from Phospholipid Membranes by Steered Molecular
	Dynamics},
  journal = JMM,
  year = {1997},
  volume = {3},
  pages = {473--475}
}

@INPROCEEDINGS{SZGG97,
  author = {Q. F. Stout and D. L. de Zeeuw and T. I. Gombosi and C. P. T. Groth
	and H.G. Marshall and K.G. Powell},
  title = {Adaptive Blocks: A High Performance Data Structure},
  booktitle = {Proceedings of Supercomputing~'97},
  year = {1997}
}

@PHDTHESIS{Stre97,
  author = {C. Streit},
  title = {{BOOGA}, ein Komponentenframework f{\"u}r Grafikanwendungen},
  school = {Institute of Computer Science and Applied Mathematics, University
	of Berne},
  year = {1997}
}

@BOOK{Stro97,
  title = {The {C}++ Programming Language},
  publisher = {Addison-Wesley},
  year = {1997},
  author = {B. Stroustrup},
  address = {Reading, Massachusetts},
  edition = {Third}
}

@ARTICLE{SUKH97,
  author = {Sergei I. Sukharev and P. Blount and B. Martinac and C. Kung},
  title = {Mechanosensitive channels of {\it {E}scherichia {C}oli} - The {MscL}
	gene, protein, and activities},
  journal = {Annual Review of Physiology},
  year = {1997},
  volume = {69},
  pages = {633--657}
}

@ARTICLE{SWIN97,
  author = {David C. Swinney and Amy Y. Mak and Jim Barnett and Chakkodabylu
	S. Ramesha},
  title = {{Differential Allosteric Regulation of Prostaglandin H Synthase 1
	and 2 by Arachidonic Acid}},
  journal = JBC,
  year = {1997},
  volume = {272},
  pages = {12393--12398},
  number = {19}
}

@ARTICLE{TIPP97,
  author = {D.~B.~Tippin and M.~Sundaralingam.},
  title = {Comparison of major groove hydration in isomorphus {A-DNA} octamers
	and dependence on base sequence and local helix geometry},
  journal = BCH,
  year = {1997},
  volume = {36},
  pages = {536--543}
}

@ARTICLE{TIRA97,
  author = {Julian Tirado-Rives and Modesto Orozco and William Jorgensen},
  title = {Molecular dynamics simulations of the unfolding of barnase in water
	and 8{M} aqueous urea},
  journal = BCH,
  year = {1997},
  volume = {36},
  pages = {7313--7329}
}

@ARTICLE{TSKH97,
  author = {L. Tskhovrebova and J. Trinick and J.A. Sleep and R.M. Simmons},
  title = {Elasticity and unfolding of single molecules of the giant protein
	titin},
  journal = NAT,
  year = {1997},
  volume = {387},
  pages = {308--312}
}

@ARTICLE{UNGE97,
  author = {Vinzenz M. Unger and P. A. Hargrave and J. M. Baldwin and Gebhard
	F. X. Schertler},
  title = {Arrangement of Rhodopsin Transmembrane $\alpha$-Helices},
  journal = NAT,
  year = {1997},
  volume = {389},
  pages = {203--206}
}

@ARTICLE{HELE97,
  author = {V. Helenius, R. Monshouwer and R. {van Grondelle}},
  title = {Temperature-dependent lifetimes and quantum yield of the singlet
	and triplet states of the B820 subunit of LHI Antenna complex of
	purple bacterium {\em Rhodospirillum rubrum}},
  journal = {J.~Phys.~Chem.~B},
  year = {1997},
  volume = {101},
  pages = {10554--10559}
}

@ARTICLE{VOLO97,
  author = {A. V. Vologodskii and John F. Marko},
  title = {Extension of Torsionally Stressed DNA by External Force},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {123--132}
}

@ARTICLE{VoSc97,
  author = {Y. N. Vorobjev and H. A. Scheraga},
  title = {A fast adaptive multigrid boundary element method for macromolecular
	electrostatic computations in a solvent},
  journal = {Journal of Computational Chemistry},
  year = {1997},
  volume = {18},
  pages = {569--583},
  annote = {A fast multigrid boundary element (MBE) method for solving the Poisson
	equation for macromolecular electrostatic calculations in a solvent
	is developed. To convert the integral equation of the BE method into
	a numerical linear equation of low dimensions, the MBE method uses
	an adaptive tesselation of the molecular surface by BEs with nonregular
	size. The size of the BEs increases in three successive levels as
	the uniformity of the electrostatic field on the molecular surface
	increases. The MBE method provides a high degree of consistency,
	good accuracy, and stability when the sizes of the BEs are varied.
	The computational complexity of the unrestricted MBE method scales
	as O(Nat), where Nat is the number of atoms in the macromolecule.
	The MBE method is ideally suited for parallel computations and for
	an integrated algorithm for calculations of solvation free energy
	and free energy of ionization, which are coupled with the conformation
	of a solute molecule. The current version of the 3-level MBE method
	is used to calculate the free energy of transfer from a vacuum to
	an aqueous solution and the free energy of the equilibrium state
	of ionization of a 17-residue peptide in a given conformation at
	a given pH in 400 s of CPU time on one node of the IBM SP2 supercomputer.}
}

@ARTICLE{Vote97a,
  author = {A.~Voter},
  title = {A method for accelerating the molecular dynamics simulation of infrequent
	events},
  journal = JCP,
  year = {1997},
  volume = {106},
  pages = {4665--4677},
  number = {11}
}

@ARTICLE{Vote97b,
  author = {A.~F.~Voter},
  title = {Hyperdynamics: accelerated molecular dynamics of infrequent events},
  journal = PRL,
  year = {1997},
  volume = {78},
  pages = {3907}
}

@ARTICLE{WADE97,
  author = {R.H. Wade and A.A. Hyman},
  title = {Microtubule structure and dynamics},
  journal = COCB,
  year = {1997},
  volume = {9},
  pages = {12--17}
}

@ARTICLE{WAGE97,
  author = {T. Wagenknecht and M. Radermacher},
  title = {Ryanodine receptors: Structure and macromolecular interactions},
  journal = COSB,
  year = {1997},
  volume = {7},
  pages = {258--265}
}

@ARTICLE{WaKG98,
  author = {W. L. Walker and M. L. Kopka and D. S. Goodsell},
  title = {Progress in design of {DNA} sequence-specific Lexitropsins},
  journal = {Biopolymers},
  year = {1997},
  volume = {44},
  pages = {323--334}
}

@ARTICLE{WALZ97,
  author = {T. Walz and R. Ghosh},
  title = {Two-dimensional crystallization of the light-harvesting {I} - Reaction
	centre photounit from {{\em {R}hodospirillum rubrum}}},
  journal = JMB,
  year = {1997},
  volume = {265},
  pages = {107--111}
}

@CONFERENCE{WAKS97,
  author = {D. C. Wang and A. W. Appel and J. L. Korn and C. S. Serra},
  title = {The {Z}ephyr {A}bstract {S}yntax {D}escription {L}anguage},
  booktitle = {Proceedings of USENIX Conference on Domain-Specific Languages},
  year = {1997},
  publisher = {Santa Barbara, CA}
}

@ARTICLE{WEDE97a,
  author = {G.J. Wedemeyer and P.A. Patten and L.H. Wang and P.G. Schultz and
	R.C. Stevens},
  title = {Structural Insights into the Evolution of an Antibody Combining Site},
  journal = {Science },
  year = {1997},
  volume = {276},
  pages = {1665--1669}
}

@ARTICLE{WEDE97,
  author = {G.J. Wedemeyer and L.H. Wang and P.A. Patten and P.G. Schultz and
	R.C. Stevens},
  title = {Crystal Structure of the Free and Liganded Form of an Esterolytic
	Catalytic Antibody},
  journal = JMB,
  year = {1997},
  volume = {268},
  pages = {390--400}
}

@ARTICLE{WIDO97,
  author = {J.~Widom},
  title = {Chromosome Structure and Gene Regulation},
  year = {1997},
  note = {Submitted}
}

@INPROCEEDINGS{WILT97,
  author = {Wolfgang Wiltschko and Ursula Munro and Roswitha Wiltschko},
  title = {Magnetoreception in Migratory Birds: Light-Mediated and Magnetite-Mediated
	Processes?},
  booktitle = {RIN 1997:Orientation \&Navigation - Birds, Humans and other Animals},
  year = {1997}
}

@ARTICLE{WOEH97,
  author = {G. Woehlke and A.K. Ruby and C.L. Hart and B. Ly and N. Hom-Boohrer
	and R.D. Vale},
  title = {Microtubule interaction site of the kinesin motor},
  journal = CEL,
  year = {1997},
  volume = {90},
  pages = {207--216}
}

@ARTICLE{WOOD97,
  author = {J.R. Woodward and R.J. Jackson and C.R. Timmel and P.J. Hore and
	K.A. McLauchlan},
  title = {Resonant radiofrequency magnetic field effects on a chemical reaction},
  journal = {Chem.~Phys.~Lett.},
  year = {1997},
  volume = {272},
  pages = {376--382}
}

@ARTICLE{WOOL97,
  author = {T.~B.~Woolf and B.~Roux},
  title = {The binding site of sodium in the gramacidin {A} channel: comparison
	of molecular dynamics with solid-state {NMR} data},
  journal = BJ,
  year = {1997},
  volume = {72},
  pages = {1930--1945},
  annote = {Describes method of using induced polarization for ion-peptide interactions}
}

@ARTICLE{WRIG97,
  author = {Willy Wriggers and Klaus Schulten },
  title = {Protein Domain Movements: {D}etection of Rigid Domains and Visualization
	of Hinges in Comparisons of Atomic Coordinates},
  journal = PRO,
  year = {1997},
  volume = {29},
  pages = {1--14},
  number = {1}
}

@ARTICLE{WRIG97A,
  author = {Willy Wriggers and Klaus Schulten },
  title = {Stability and Dynamics of {G}-actin: {B}ack Door Water Diffusion
	and Behavior of a subdomain {3/4} loop},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {624--639}
}

@ARTICLE{WU97B,
  author = {H.-M. Wu and I.-J. Lee and R.J. Cogdell and G.J. Small},
  title = {Exciton level structure and energy disorder of the {B}850 ring of
	the {LH}2 antenna complex},
  journal = {J.~Phys.~Chem.~B},
  year = {1997},
  volume = {101},
  pages = {7654--7663}
}

@ARTICLE{WU97A,
  author = {H.-M. Wu and M. Ratsep and R. Jankowiak and R.J. Cogdell and G.J.
	Small},
  title = {Comparison of the {LH}2 antenna complexes of {\em {R}hodopseudomonas
	acidophila} (Strain 10050) and {\em {R}hodobacter sphaeroides} by
	high-pressure absorption, high-pressure hole burning, and temperature-dependent
	absorption spectroscopies},
  journal = {J.~Phys.~Chem.~B},
  year = {1997},
  volume = {101},
  pages = {7641--7653}
}

@ARTICLE{WU97,
  author = {H.-M. Wu and N. R. S. Reddy and G. J. Small},
  title = {Direct Observation and Hole Burning of the Lowest Exciton Level ({B}870)
	of the LH2 Antenna Complex of {{\em Rhodopseudomonas acidophila}}
	(Strain 10050) },
  journal = JPCB,
  year = {1997},
  volume = {101},
  pages = {651--656}
}

@ARTICLE{XIA97,
  author = {D. Xia and C.-A. Yu and H. Kim and J.-Z. Xia and A. M. Kachurin and
	L. Zhang and L. Yu and J. Deisenhofer},
  title = {Crystal structure of the cytochrome bc$_1$ complex from bovine heart
	mitochondria},
  journal = SCI,
  year = {1997},
  volume = {277},
  pages = {60--66}
}

@ARTICLE{XuHS97,
  author = {Z.~Xu and A.~L.~Horwich and P.~B.~Sigler},
  title = {The crystal structure of the assymmetric {G}ro{EL}-{G}ro{ES}-$({ADP})_{7}$
	chaperonin complex},
  journal = NAT,
  year = {1997},
  volume = {388},
  pages = {741--750}
}

@ARTICLE{YOUN97,
  author = {M.~A.~Young and B.Jayaram and D.~L.~Beveridge.},
  title = {Intrusion of counterions into the spine of hydration in the minor
	groove of {B-DNA}: fractional occupancy of electronegative pockets},
  journal = JACS,
  year = {1997},
  volume = {119},
  pages = {59--69}
}

@ARTICLE{YOUN97A,
  author = {M.~A.~Young and G.~Ravishanker and D.~L.~Beveridge.},
  title = {A 5-nanosecond molecular dynamics trajectory for {B-DNA}: analysis
	of structure, motion and solvation},
  journal = BJ,
  year = {1997},
  volume = {73},
  pages = {2313--2336}
}

@INPROCEEDINGS{ZELL97B,
  author = {Michael Zeller and James C. Phillips and Andrew Dalke and William
	Humphrey and Klaus Schulten and Rajeev Sharma and T. S. Huang and
	V. I. Pavlovic and Y. Zhao and Z. Lo and S. Chu},
  title = {A Visual Computing Environment for Very Large Scale Biomolecular
	Modeling},
  booktitle = {Proceedings of the 1997 {IEEE} International Conference on Application-specific
	Systems, Architectures and Processors {(ASAP)}},
  year = {1997},
  pages = {3--12},
  publisher = {{IEEE} Computer Society Press},
  annote = {An invited paper.}
}

@INCOLLECTION{ZELL97,
  author = {Michael Zeller and Rajeev Sharma and Klaus Schulten},
  title = {Vision-Based Robot Motion Planning Using a Topology Representing
	Neural Network},
  booktitle = {Applications of Neural Adaptive Control Technology},
  publisher = {World Scientific Publishing},
  year = {1997},
  editor = {Jens Kalkkuhl and Ken Hunt and Rafal Zbikowski and Andrzej Dzielinski},
  volume = {17},
  series = {World Scientific Series in Robotics and Intelligent Systems},
  pages = {181--204}
}

@INPROCEEDINGS{ZELL97A,
  author = {Michael Zeller and Rajeev Sharma and Klaus Schulten},
  title = {Learning the Perceptual Control Manifold for Sensor-Based Robot Path
	Planning},
  booktitle = {Proceedings of the 1997 {IEEE} International Symposium on Computational
	Intelligence in Robotics and Automation {(CIRA'97)}},
  year = {1997},
  pages = {48--53},
  publisher = {{IEEE} Computer Society Press}
}

@ARTICLE{ZELL97C,
  author = {Michael Zeller and Rajeev Sharma and Klaus Schulten},
  title = {Motion Planning of a Pneumatic Robot Using a Neural Network},
  journal = {IEEE Control Systems Magazine},
  year = {1997},
  volume = {17},
  pages = {89--98}
}

@ARTICLE{ZhSk97,
  author = {Meiqing Zhang and R.~D. Skeel},
  title = {Cheap Implicit Symplectic Integrators},
  journal = {Appl.\ Num.\ Math.},
  year = {1997},
  volume = {25},
  pages = {297--302}
}

@ARTICLE{ZhBe97,
  author = {R. H. Zhou and B. J. Berne},
  title = {Smart Walking---a New Method for {B}oltzmann Sampling of Protein
	Conformations},
  journal = {J. Chem.\ Phys.},
  year = {1997},
  volume = {107},
  pages = {9185--9196},
  number = {21}
}

@ARTICLE{ZBLH97,
  author = {S. J. Zhou and D. M. Beazley and P. S. Lomdahl and B. L. Holian},
  title = {Large-Scale Molecular Dynamics Simulations of Three-Dimensional Ductil
	Failure},
  journal = {Physical Review Letters},
  year = {1997},
  volume = {78},
  pages = {479--482}
}

@PHDTHESIS{Clar96,
  author = {Terry W. Clark},
  title = {A Parallel Programming Approach for Scientific Applications},
  school = {Dept.\ of Computer Science, Univ. of Houston},
  year = {1996},
  address = {Houston, Texas},
  month = DEC
}

@MANUAL{CART96,
  title = {Nucleic Acid MOdeling Tool - NAMOT 2.1},
  author = {E. Carter and C.S. Tung},
  month = AUG,
  year = {1996},
  note = {Los Alamos National Laboratory}
}

@INPROCEEDINGS{BeLo93,
  author = {P. S. Lomdahl and D. M. Beazley},
  title = {Multi-Million Particle Molecular Dynamics on {MPP}s},
  booktitle = {PARA'95, Second International Workshop},
  year = {1996},
  volume = {1041},
  series = {Lecture Notes in Computer Science},
  pages = {391--407},
  address = {Lyngby, Denmark},
  month = AUG,
  publisher = {Springer-Verlag}
}

@INPROCEEDINGS{BaLe96,
  author = {E. Barth and B. Leimkuhler},
  title = {Symplectic Methods for Conservative Multibody Systems},
  booktitle = {Integration Algorithms and Classical Mechanics},
  year = {1996},
  editor = {Jerrold E. Marsden and George W. Patrick and William F. Shadwick},
  volume = {10},
  series = {Fields Institute Communications},
  pages = {25--43},
  month = JUL,
  organization = {Fields Institute},
  publisher = AMS
}

@INPROCEEDINGS{Beaz96,
  author = {D.~M. Beazley},
  title = {{SWIG}: An Easy to Use Tool for Integrating Scripting Languages with
	{C} and {C\texttt{++}}},
  booktitle = {Proceeding of The Forth Annual Tcl/Tk Workshop '96},
  year = {1996},
  pages = {129--139},
  month = JUL,
  organization = {USENIX Association}
}

@BOOK{Leac96,
  title = {Molecular Modelling: Principles and Applications},
  publisher = {Addison-Wesley},
  year = {1996},
  author = {Andrew R. Leach},
  address = {Reading, Massachusetts},
  month = JUL,
  nremark = {0-582-23933-8}
}

@INPROCEEDINGS{McLa96,
  author = {Robert I. McLachlan},
  title = {More on Symplectic Correctors},
  booktitle = {Integration Algorithms and Classical Mechanics},
  year = {1996},
  editor = {Jerrold E. Marsden and George W. Patrick and William F. Shadwick},
  volume = {10},
  series = {Fields Institute Communications},
  pages = {141--149},
  month = JUL,
  organization = {Fields Institute},
  publisher = AMS,
  nremark = {manuscript received May 18, 1994}
}

@INPROCEEDINGS{McSc96,
  author = {Robert I. McLachlan and C. Scovel},
  title = {A Survey of Open Problems in Symplectic Integration},
  booktitle = {Integration Algorithms and Classical Mechanics},
  year = {1996},
  editor = {Jerrold E. Marsden and George W. Patrick and William F. Shadwick},
  volume = {10},
  series = {Fields Institute Communications},
  pages = {151--180},
  month = JUL,
  organization = {Fields Institute},
  publisher = AMS
}

@INPROCEEDINGS{Sanz96,
  author = {J. M. Sanz-Serna},
  title = {Backward Error Analysis of Symplectic Integrators},
  booktitle = {Integration Algorithms and Classical Mechanics},
  year = {1996},
  editor = {Jerrold E. Marsden and George W. Patrick and William F. Shadwick},
  volume = {10},
  series = {Fields Institute Communications},
  pages = {193--205},
  month = JUL,
  organization = {Fields Institute},
  publisher = AMS
}

@INPROCEEDINGS{WiHT96,
  author = {J. Wisdom and M. Holman and J. Touma},
  title = {Symplectic Correctors},
  booktitle = {Integration Algorithms and Classical Mechanics},
  year = {1996},
  editor = {Jerrold E. Marsden and George W. Patrick and William F. Shadwick},
  volume = {10},
  series = {Fields Institute Communications},
  pages = {217--244},
  month = JUL,
  organization = {Fields Institute},
  publisher = AMS,
  nremark = {manuscript dated January 26, 1994, does not seem to permit long timesteps;
	eq.~(3) should not have the factor $1/(2\pi)$.}
}

@INCOLLECTION{LoSS96b,
  author = {M. L{\'o}pez-Marcos and J. M. Sanz-Serna and R.~D. Skeel},
  title = {Explicit Symplectic Integrators with Maximal Stability Intervals},
  booktitle = {Numerical Analysis, {A}. {R}. {M}itchell 75th Birthday Volume},
  publisher = {World Scientific},
  year = {1996},
  editor = {D. F. Griffiths and G. A. Watson},
  pages = {163--176},
  address = {Singapore},
  month = JUN,
  nack = {Iber, doensf, nsfarpa, nih},
  nremark = {ISBN: 981-02-2719-1}
}

@MISC{John96,
  author = {R.~E. Johnson},
  title = {Frameworks},
  howpublished = {Seminar, Z{\"u}hlke Informatik, Z{\"u}rich},
  month = MAY,
  year = {1996}
}

@INPROCEEDINGS{KALE96,
  author = {L. V. Kale and Milind Bhandarkar and Narain Jagathesan and Sanjeev
	Krishnan and Joshua Yelon},
  title = {{Converse: An Interoperable Framework for Parallel Programming}},
  booktitle = {Proceedings of the 10th International Parallel Processing Symposium},
  year = {1996},
  pages = {212--217},
  address = {Honolulu, Hawaii},
  month = APR
}

@UNPUBLISHED{Seil96,
  author = {Werner M. Seiler},
  title = {On the numerical integration of constrained {H}amiltonian systems
	using Dirac brackets},
  month = MAR,
  year = {1996}
}

@TECHREPORT{Reic96b,
  author = {S. Reich},
  title = {Smoothed {L}angevin Dynamics of Highly Oscillatory Systems},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1996},
  number = {SC 96-04},
  month = FEB
}

@ARTICLE{SPOE96,
  author = {D. {van\,der\,Spoel} and B. L. {de\,Groot} and S. Hayward and H.
	J. C. Berendsen and H. J. Vogel},
  title = {Bending of the Calmodulin Central Helix: A Theoretical Study},
  journal = PS,
  year = {1996},
  volume = {5},
  pages = {2044--2053}
}

@BOOK{Otti96,
  title = {Stochastic Process in Polymeric Fluids},
  publisher = {Springer-Verlag},
  year = {1996},
  author = {H.C. {{\"O}ttinger}},
  address = {New York},
  annote = {More theoretical treatment of stochastic differential equation that
	that of Gardiner. Develop higher order method for solving stochastic
	diff. eq. Application to polymeric systems.}
}

@ARTICLE{AGBF96,
  author = {D.~M.~F.~van Aalten and B.~L.~de Groot and H.~Berendsen and J.~B.~C.~Findlay},
  title = {Conformational analysis of retinoids and restriction of their dynamics
	by retinoid--binding proteins},
  journal = BCHJ,
  year = {1996},
  volume = {319},
  pages = {543--550}
}

@ARTICLE{Abra96,
  author = {Jan Pieter Abrahams and Susan K. Buchanan and Mark J.~van Raaij and
	Ian M. Fearnley and Andrew G.W. Leslie and John E. Walker},
  title = {The structure of the bovine F$_1$-ATPase complexed with the pepide
	antibiotic efrapeptin},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {6420--6424}
}

@ARTICLE{AKIM96,
  author = {S. Akimoto and S. Takaichi and T. Ogata and Y. Nishimura and I Yamazaki
	and M. Mimuro},
  title = {Excitation energy transfer in carotenoid-chlorophyll protein complexes
	probed by femtosecond fluorescence decays},
  journal = CPL,
  year = {1996},
  volume = {260},
  pages = {147--152}
}

@ARTICLE{ALLE96,
  author = {Phillip G. Allen and Lorraine E. Laham and Michael Way and Paul A.
	Janmey},
  title = {Binding of Phosphate, Aluminum Fluoride, or Beryllium Fluoride to
	{F}-actin Inhibits Severing by Gelsolin},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {4665--4670}
}

@ARTICLE{ANDE96,
  author = {P.O. Andersson and R.J. Cogdell and T. Gillbro},
  title = {Femtosecond dynamics of carotenoid-to-bacteriochlorophyll $a$ energy
	transfer in the light-harvesting antenna complexes from the purple
	bacterium {\em {C}hromation purpuratum}},
  journal = {Chem.~Phys.},
  year = {1996},
  volume = {210},
  pages = {195--217},
  annote = {Car-BChl transfer in {\em Chromatium purpuratum}}
}

@ARTICLE{AnSt96,
  author = {I. Andricioaei and J. E. Straub},
  title = {Generalized Simulated Annealing Algorithms Using {T}sallis Statistics:
	Application to Conformational Optimization of a Tetrapeptide},
  journal = pre,
  year = {1996},
  volume = {53},
  pages = {R3055--R3058},
  annote = {A generalized MC algorithm that samples equilibrium Tsallis statistical
	distributions is presented. The relative effiicency of a simulated
	annealing protocol employing the generalized {M}onte {C}arlo algorithm
	is shown to be significantly more effective than MD or HMC based
	annealing algorithms in isolating the global energy minimum of a
	tetrapeptide}
}

@ARTICLE{ARLT96,
  author = {T. Arlt and M. Bibikova and H. Penzkofer and D. Oesterhelt and W.
	Zinth},
  title = {Strong Acceleration of Primary Photosynthetic Electron Transfer in
	a Mutated Reaction Center of {\em Rhodopseudomonas viridis}},
  journal = JPC,
  year = {1996},
  volume = {1996},
  pages = {12060--12065}
}

@ARTICLE{ARNA96,
  author = {I. Arnal and F. Metoz and S. DeBonis and R.H. Wade},
  title = {Three-dimensional structure of functional motor proteins on microtubules},
  journal = CB,
  year = {1996},
  volume = {6},
  pages = {1265--1270}
}

@ARTICLE{AuLW96,
  author = {P. Auffinger and S. Louise-May and E. Westof},
  title = {Molecular Dynamics Simulations of the Anticodon Hairpin Loop of rRNA$^{\rm
	Asp}$. Structuring Effects of C--H$\cdots$O Hydrogen Bonds and Long-Range
	Hydration Forces},
  journal = {J. Amer.\ Chem.\ Soc.},
  year = {1996},
  volume = {118},
  pages = {1181--1189}
}

@ARTICLE{BAIL96,
  author = {C. Bailly and D. Payet and A. A. Travers and M. J. Waring},
  title = {{PCR-based} development of {DNA} substrates containing modified bases:
	{An} efficient system for investigating the role of the exocyclic
	groups in chemical and structural recognition by minor groove binding
	drugs and proteins},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {13623--13628}
}

@ARTICLE{BALJ96,
  author = {R. C. Arlette Baljon and M. O. Robbins},
  title = {Energy Dissipation During Rupture of Adhesive Bonds},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {482--484}
}

@ARTICLE{BaBR96,
  author = {P. Ballestrero and P. Baglietto and C. Ruggiero},
  title = {Molecular Dynamics for Proteins: Performance Evaluation on Massively
	Parallel Computers Based on Mesh Networks Using a Space Decomposition
	Approach},
  journal = JCC,
  year = {1996},
  volume = {17},
  pages = {469--475},
  number = {4}
}

@ARTICLE{BALL96,
  author = {R. M. Ballew and J. Sabelko and M Gruebele},
  title = {Direct observation of fast protein folding: The initial collapse
	of apomyoglobin},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1996},
  volume = {93},
  pages = {5759--5764}
}

@ARTICLE{BALL96a,
  author = {R. M. Ballew and J. Sabelko and M. Gruebele},
  title = {Observation of distinct nanosecond and microsecond protein folding
	events},
  journal = {Nature Struct.\ Bio.},
  year = {1996},
  volume = {3},
  pages = {923--926},
  number = {11}
}

@ARTICLE{BALS96,
  author = {Manel A. Balsera and Willy Wriggers and Yoshitsugu Oono and Klaus
	Schulten},
  title = {Principal Component Analysis and Long Time Protein Dynamics},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {2567--2572},
  number = {7},
  annote = {there is no BI techreport on this one yet}
}

@ARTICLE{BARN96,
  author = {S.~M.~Barnett and S.~Dracheva and R.~W.~Hendler and I.~W.~Levin},
  title = {Lipid-induced conformational changes of an integral membrane protein:
	An infrared spectroscopic study of the effects of triton X-100 treatment
	on the purple membrane of Halobacterium halobium ET1001},
  journal = {Biochemistry},
  year = {1996},
  volume = {35},
  pages = {4558--4567}
}

@INCOLLECTION{BaMS96,
  author = {E. Barth and M. Mandziuk and T. Schlick},
  title = {A Separating Framework for Increasing the Timestep in Molecular Dynamics},
  booktitle = {Computer Simulation of Biomolecular Systems: Theoretical and Experimental
	Applications},
  publisher = {ESCOM},
  year = {1996},
  editor = {W.~F. van Gunsteren and P.~K. Weiner and A.~J. Wilkinson},
  volume = {3},
  chapter = {4},
  pages = {97--121},
  address = {Leiden, The Netherlands}
}

@ARTICLE{BART96,
  author = {N.R. Barton and L.S.B. Goldstein},
  title = {Going mobile: Microtubule motors and chromosome segregation},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {1735--1742}
}

@ARTICLE{BAUD96,
  author = {J.~Baudry and S.~Crouzy and B.~Roux and J.C.~Smith},
  title = {Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational
	Energetics},
  journal = JCICS,
  year = {1996},
  volume = {37},
  pages = {1018--1024}
}

@ARTICLE{BEAS96,
  author = {R.C. Beason and P. Semm},
  title = {Does the avian ophthalmic nerve carry magnetic navigational information?},
  journal = {J.~Exp.~Biol.},
  year = {1996},
  volume = {199},
  pages = {1241--1244}
}

@ARTICLE{BEAT96A,
  author = {M.~Beato and R.~Candau and S.~Ch{\'a}vez and C.~M{\"o}ws and M.~Truss},
  title = {Interaction of steroid hormone receptors with transcription factors
	involves chromatin remodelling},
  journal = JSBMB,
  year = {1996},
  volume = {56},
  pages = {47--59},
  number = {1--6}
}

@ARTICLE{BEAT96,
  author = {M.~Beato and S.~Ch{\'a}vez and M.~Truss},
  title = {Transcriptional regluation by steroid hormones},
  journal = {Steroids},
  year = {1996},
  volume = {61},
  pages = {240--251}
}

@INPROCEEDINGS{BeLo96,
  author = {D. M. Beazley and P. S. Lomdahl},
  title = {Lightweight Computational Steering of Very Large Scale Molecular
	Dynamics Simulations},
  booktitle = {Proceedings of Supercomputing~'96},
  year = {1996}
}

@ARTICLE{BILL96,
  author = {Martin Billeter and Peter G{\"u}ntert and Peter Luginb{\"u}hl and
	Kurt W{\"u}thrich},
  title = {Hydration and {DNA} recognition by homeodomains},
  journal = {Cell},
  year = {1996},
  volume = {85},
  pages = {1057--1065}
}

@ARTICLE{BISH96,
  author = {Thomas C. Bishop and Klaus Schulten},
  title = {Molecular Dynamics Study of Glucocorticoid Receptor--{DNA} Binding},
  journal = PRO,
  year = {1996},
  volume = {24},
  pages = {115--133},
  number = {1},
  tbtechrep = {TB-95-07}
}

@ARTICLE{BLOC96,
  author = {S.M. Block},
  title = {Fifty ways to love your lever: Myosin motors},
  journal = CEL,
  year = {1996},
  volume = {87},
  pages = {151--157}
}

@ARTICLE{Blun96,
  author = {T. Blundell},
  title = {Structure-based Drug Design},
  journal = NAT,
  year = {1996},
  volume = {384},
  pages = {23--26}
}

@ARTICLE{BOOT96,
  author = {Paula J. Booth and Amjad Farooq and Sabine L. Flitsch},
  title = {Retinal Binding During Folding and Assembly of the Membrane Protein
	Bacteriorhodopsin},
  journal = BCH,
  year = {1996},
  volume = {35},
  pages = {5902--5909}
}

@ARTICLE{BREE96,
  author = {J. Breed and R. Sankararamakrishnan and I. D. Kerr and M. S. P. Sansom},
  title = {Molecular dynamics simulations of water within models of ion channels},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {1643--1661}
}

@ARTICLE{BROC96,
  author = {Brian Brocklehurst and Keith A. McLaughlan},
  title = {Free radical mechanism for the effects of environmental electromagnetic
	fields on bioloical systems},
  journal = {Int.~J.~Rad.~Biol.},
  year = {1996},
  volume = {69},
  pages = {3--24}
}

@ARTICLE{BrMa96,
  author = {R.~D. Brown and Y.~C. Martin},
  title = {Use of Structure-Activity Data to Compare Structure-Based Clustering
	Methods and Descriptors for Use in Compound Selection},
  journal = JCICS,
  year = {1996},
  volume = {36},
  pages = {572--584}
}

@ARTICLE{BRUN96,
  author = {A. Br{\"u}nger},
  title = {Patterson Correlation Searches and Refinement},
  journal = {Methods in Enzymology},
  year = {1996},
  note = {In press}
}

@ARTICLE{BUST96,
  author = {M. Bustin and R. Reeves},
  title = {{High-Mobility-Group} chromosomal proteins: {A}rchitectural components
	that facilitate chromatin function},
  journal = {Progress in Nucleic Acid Research and Molecular Biology},
  year = {1996},
  volume = {54},
  pages = {35--100}
}

@ARTICLE{CALL96,
  author = {Ondine H. Callan and On-Yee So and David C. Swinney},
  title = {The Kinetic Factors That Determine the Affinity and Selectivity for
	Slow Binding Inhibition of Human Prostaglandin {H} Synthase 1 and
	2 by Indomethacin and Flurbiprofen},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {3548--3554},
  number = {7}
}

@ARTICLE{CANA96,
  author = {M.~A.~Canady and S.~B.~Larson and J.~Day and A.~McPherson},
  title = {Crystal structure of turnip yellow mosaic virus},
  journal = {Nature Structural Biology},
  year = {1996},
  volume = {3},
  pages = {771--781},
  number = {9}
}

@ARTICLE{CANF96,
  author = {J.M. Canfield and R.L. Belford and P.G. Debrunner},
  title = {Calculations of Earth-strength steady and oscillating magnetic field
	effects in coenzyme {B}$_{12}$ radical pair systems},
  journal = {Mol.~Phys.},
  year = {1996},
  volume = {89},
  pages = {889--930}
}

@ARTICLE{CHTR96,
  author = {C-K. Chan and Y. Hu and S. Takahashi and D. L. Rousseau and W. A.
	Eaton and J. Hofrichter},
  title = {Protein folding kinetics studied by ultrafast mixing},
  journal = {Biophys. J.},
  year = {1996},
  volume = {70},
  pages = {A177}
}

@ARTICLE{CHEAT96,
  author = {T.~E.~Cheatham and P.~A.~Kollman},
  title = {Observation of the {A-DNA} to {B-DNA} transition during unrestrained
	molecular dynamics in aqueous solution.},
  journal = JMB,
  year = {1996},
  volume = {259},
  pages = {434--444}
}

@ARTICLE{CHIK96,
  author = {J. K. Chik and U. Lindberg and C. E. Schutt},
  title = {The structure of an open state of beta actin at 2.65\,{{\AA}} resolution},
  journal = JMB,
  year = {1996},
  volume = {263},
  pages = {607--623}
}

@ARTICLE{CLAD96,
  author = {Josep Cladera and Jaume Torres and Esteve Padr{\'o}s},
  title = {Analysis of Conformational Changes in Bacteriorhodopsin Upon Retinal
	Removal},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {2882--2887}
}

@ARTICLE{CLAY96,
  author = {A.H.A. Clayton and G.D. Scholes and K.P. Ghiggino and M.N. Padden-Row},
  title = {Through-bond and through-space coupling in photoinduced electron
	and energy transfer: an {\em ab initio} and semiempirical study},
  journal = {J.~Phys.~Chem.},
  year = {1996},
  volume = {100},
  pages = {10912--10918}
}

@ARTICLE{CLOB07,
  author = {Max W. Chang and William Lindstrom and Arthur J. Olson and Richard K. Belew},
  title = {Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries},
  journal = {Journal of Chemical Information and Modeling},
  year = {2007},
  URL = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci700044s},
  ISSN = {1549-9596}
}


@ARTICLE{CLUZ96,
  author = {Phillipe Cluzel and Anne Lebrun and Christoph Heller and Richard
	Lavery and Jean-Louis Viovy and Didier Chatenay and Fran{\c c}ois
	Caron},
  title = {{DNA}: {A}n Extensible Molecule},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {792--794}
}

@ARTICLE{COGD96,
  author = {R.J. Cogdell and P.K. Fyfe and S.J. Barrett and S.M. Prince and A.A.
	Freer and N.W. Isaacs and P. McGlynn and C.N. Hunter},
  title = {The purple bacterial photosynthetic unit},
  journal = PHOR,
  year = {1996},
  volume = {48},
  pages = {55--63}
}

@ARTICLE{CoIx96,
  author = {John P. Coleman and Liviu Gr.\ Ixaru},
  title = {{P}-Stability and Exponential Fitting Methods for $y'' = f(x, y)$},
  journal = {IMA J. Numer.\ Anal.},
  year = {1996},
  volume = {16},
  pages = {179--199}
}

@ARTICLE{CREV96,
  author = {I.M.-T.C. Crevel and A. Lockhart and R.A. Cross},
  title = {Weak and strong states of kinesin and ncd},
  journal = JMB,
  year = {1996},
  volume = {257},
  pages = {66--76}
}

@ARTICLE{CuCC96,
  author = {S. T. Cui and P. T. Cummings and H. D. Cochran},
  title = {Multiple Time Step Nonequilibrium Molecular Dynamics Simulation of
	the Rheological Properties of Liquid $n$-Decane},
  journal = {J. Chem.\ Phys.},
  year = {1996},
  volume = {104},
  pages = {255--262},
  number = {1},
  nabstract = {Nonequilibrium and equilibrium molecular dynamics simulations are
	reported for a united-atom model of n-decane at a state point in
	the liquid phase. The viscosity calculated by our nonequilibrium
	molecular dynamics simulations is in good agreement with that obtained
	from our equilibrium molecular dynamics simulations via the Green-Kubo1
	relation and with that obtained by Mundy ct al. `J. Chem. Phys. 102,
	3776 (1995) using the same potential model at the same state conditions.
	Additionally, the viscosity calculated by nonequilibrium molecular
	dynamics is in very good agreement with experimental results for
	n-decane. The algorithm used for the equilibrium molecular dynamics
	simulations is an application to alkanes of the multitime step Nose
	dynamics algorithm developed by Tuckerman and Berne. For the nonequilibrium
	molecular dynamics simulations, an extension of the multitime step
	method is derived for the nonequilibrium equations of motion describing
	planar Couette flow with Nose thermostat. The contributions of the
	intramolecular interactions to the stress tensor and its relaxation
	have been analyzed; the bond stretching motions play a dominant role
	in the short-time behavior of the atomic stress-stress correlation.
	(C) 1996 American Institute of Physics.}
}

@ARTICLE{DAVI96,
  author = {W. S. Davidson and T. Hazlett and W. W. Mantulin and A. Jonas},
  title = {The Role of Apolipoprotein {A-I} Domains in Lipid Binding},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {13605--13610}
}

@ARTICLE{DAVI96A,
  author = {C. M. Davis and P. S. Parkes-Loach and C. K. Cook and K. A. Meadows
	and M. Bandilla and H. Scheer and P. A. Loach},
  title = {Comparison of the structural requirements for bacteriochlorophyll
	binding in the core light-harvesting complexes of {{\em Rhodospirillum
	rubrum}} and {{\em Rhodospirillum sphaeroides}} using reconstitution
	methodology with bacteriochlorophyll analogs.},
  journal = BCH,
  year = {1996},
  volume = {35},
  pages = {3972--84}
}

@ARTICLE{DeSk96,
  author = {S. DeBolt and J. Skolnick},
  title = {Evaluation of Atomic Level Mean Force Potentials via Inverse Folding
	and Inverse Refinement of Proteins Structures: Atomic Burial Position
	and Pair-wise non-bonded Interactions},
  journal = {Protein Eng.},
  year = {1996},
  pages = {637--655}
}

@ARTICLE{DYJH96,
  author = {V. Dhanaraj and Ye Qi-Zhuang and L.L. Johnson and D.J. Hupe and D.F.
	Ortwine and J.B. Dunbar and J.R. Rubin and A. Pavlovsky and C. Humblet
	and T.L. Blundell},
  title = {X-ray Structure of a Hydroxamate Inhibitor Complex of Stromelysin
	Catalytic Domain and Its Comparison With Members of the Zinc Metalloproteinase
	Superfamily},
  journal = {Structure},
  year = {1996},
  volume = {4},
  pages = {375--386}
}

@ARTICLE{DRAC96,
  author = {T.V. Dracheva and V.I. Novoderezhkin and A. Razjivin},
  title = {Exciton Delocalization in the Antenna of Purple Bacteria - Exciton
	Spectrum Calculations Using X-ray Data and Experimental Site Inhomogeneity},
  journal = {FEBS Lett.},
  year = {1996},
  volume = {387},
  pages = {81--84}
}

@ARTICLE{DREW96,
  author = {G. Drews},
  title = {Formation of the light-harvesting complex I (B870) of anoxygenic
	phototrophic purple bacteria},
  journal = {Arch.~Microbiol.},
  year = {1996},
  volume = {166},
  pages = {151--159},
  annote = {LH Assembly}
}

@ARTICLE{DRIS96,
  author = {J.~E.~Driscoll and C.~L.~Seachord and J.~A.~Lupisella and R.~P.~Darveau
	and P.~R.~Reczek},
  title = {Ligand--induced Conformational Changes in the Human Retinoic Acid
	Receptor ${\gamma}$ Detected using Monoclonal Antibodies},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {22969--22975}
}

@ARTICLE{DUBO96,
  author = {Paul F. Dubois and Konrad Hinsen and James Hugunin},
  title = {Numerical {P}ython},
  journal = CIP,
  year = {1996},
  volume = {10},
  pages = {262--267},
  number = {3}
}

@ARTICLE{DUBO96A,
  author = {Paul F. Dubois and T.-Y. Yang},
  title = {Extending {P}ython},
  journal = CIP,
  year = {1996},
  volume = {10},
  pages = {359--364},
  number = {4}
}

@ARTICLE{EDMO96,
  author = {D.T. Edmonds},
  title = {A sensitive optically-detected magnetic compass for animals},
  journal = {Proc.~Royal Soc.~B},
  year = {1996},
  volume = {263},
  pages = {295--298}
}

@ARTICLE{EICH96,
  author = {C. Eichwald and J. Walleczek},
  title = {Model for magnetic field effects on radical pair recombination in
	enzyme kinetics},
  journal = {Biopkys.~J.},
  year = {1996},
  volume = {71},
  pages = {623--631}
}

@ARTICLE{EKEN96,
  author = {K.~Ekena and K.~E.~Weis and J.~A.~Katzenellenbogen and B.~S.~Katzenellenbogen},
  title = {Identification of amino acids in the hormone binding domain of the
	human estrogen receptor important in estrogen binding.},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {20053--20059}
}

@INPROCEEDINGS{ELBE96,
  author = {Ron Elber},
  title = {Reaction Path Studies of Biological Molecules},
  booktitle = {Recent Developments in Theoretical Studies of Proteins ({A}dvanced
	Series in Physical Chemistry, {V}ol.~7)},
  year = {1996},
  editor = {Ron Elber},
  address = {Singapore},
  publisher = {World Scientific}
}

@ARTICLE{Elbe96A,
  author = {R. Elber},
  title = {Novel methods for molecular dynamics simulations},
  journal = COSB,
  year = {1996},
  volume = {6},
  pages = {232--235},
  number = {2}
}

@ARTICLE{ELCK96,
  author = {A.H. Elcock and J.A. McCammon},
  title = {The low dielectric interior of proteins is sufficient to cause major
	structural changes in {DNA} on association},
  journal = JACS,
  year = {1996},
  volume = {118},
  pages = {3787--3788}
}

@ARTICLE{ElBo96,
  author = {William D. Elliott and John A. Board, Jr.},
  title = {Fast Fourier Transform Accelerated Fast Multipole Algorithm},
  journal = SJSC,
  year = {1996},
  volume = {17},
  number = {2}
}

@BOOK{ETTE96,
  title = {Introduction to {M}atlab for Engineers and Scientists},
  publisher = {Prentice-Hall},
  year = {1996},
  author = {D. M. Etter},
  address = {Upper Saddle River, New Jersey}
}

@ARTICLE{FARR96,
  author = {David L. Farrens and Christian Altenbach and Ke Yang and Wayne L.
	Hubbell and H. Gobind Khorana},
  title = {Requirement of rigid--body motion of transmembrane helices for light
	activation of rhodopsin},
  journal = SCI,
  year = {1996},
  volume = {274},
  pages = {768--770}
}

@ARTICLE{FEHE96,
  author = {V.~A.~Feher and E.~P.~Baldwin and W.~Dahlquist},
  title = {Access of ligand to cavities within the core of a protein is rapid},
  journal = NATSB,
  year = {1996},
  volume = {3},
  pages = {516--521}
}

@ARTICLE{FELL96,
  author = {Scott E. Feller and Richard W. Pastor and Atipat Rojnuckarin and
	Stephen Bogusz and Bernard R. Brooks},
  title = {Effect of electrostatic force truncation on interfacial and transport
	properties of water},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {17011--17020},
  annote = {surface potentials, bulk water properties differ by 100\% from cutoff
	to Ewald; diffusion coefficient of TIP3P water is farther from experiment
	in Ewald than in cutoff, indicating need to reparametrize TIP3P for
	Ewald. You definitely need Ewald for membranes.}
}

@ARTICLE{FERG96,
  author = {Ferguson-Miller, S. and Babcock, G. T.},
  title = {Heme/Copper Terminal Oxidases},
  journal = CR,
  year = {1996},
  volume = {96},
  pages = {2889},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{FITT96,
  author = {J.~Fitter and R.E.~Lechner and G.~B{\"u}ldt and N.A.~Dencher},
  title = {Internal molecular motions of bacteriorhodopsin: Hydration-induced
	flexibility studied by quasielestic incoherent neutron scatering
	using oriented purple membranes},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {7600--7605}
}

@ARTICLE{FPFS96,
  author = {R.~A. Foty and C.~M. Pfleger and G.~Forgacs and M.~S. Steinberg},
  title = {Surface tensions of embryonic tissues predict their mutual envelopment
	behavior},
  journal = {Development},
  year = {1996},
  volume = {122},
  pages = {1611--1620},
  number = {5}
}

@ARTICLE{FRAN96,
  author = {H.A. Frank and R.J. Cogdell},
  title = {Carotenoids in photosynthesis},
  journal = PCPB,
  year = {1996},
  volume = {63},
  pages = {257--264}
}

@ARTICLE{FREE96,
  author = {A. Freer and S. Prince and K. Sauer and M. Papiz and A. Hawthornthwaite-Lawless
	and G. McDermott and R.J. Cogdell and N.W. Isaacs},
  title = {Pigment-pigment interactions and energy transfer in the antenna complex
	of the photosynthetic bacterium {\em Rhodopseudomonas acidophila}},
  journal = STR,
  year = {1996},
  volume = {4},
  pages = {449--462}
}

@BOOK{FrSm96,
  title = {Understanding Molecular Simulation: From Algorithms to Applications},
  publisher = {Academic Press},
  year = {1996},
  author = {Daan Frenkel and Berend Smit}
}

@ARTICLE{GKDT96,
  author = {E. Glikman and I. Kelson and N. V. Doan and H. Tietze},
  title = {An Optimized Algorithm for Molecular Dynamics Simulation of Large-Scale
	Systems},
  journal = {J. COMPUTATIONAL-PHYSICS},
  year = {1996},
  volume = {124},
  pages = {85--92},
  number = {1}
}

@ARTICLE{GoKa96,
  author = {Daniel Goldman and Tasso J. Kaper},
  title = {Nth-order operator splitting schemes and nonreversible systems},
  journal = SJNA,
  year = {1996},
  volume = {33},
  pages = {349--367},
  nremark = {It contains the explicit third-order stuff in section 6.}
}

@ARTICLE{GoSi96,
  author = {O. Gonzalez and J.C. Simo},
  title = {On the stability of symplectic and energy--momentum algorithms for
	nonlinear {H}amiltonian systems with symmetry},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  year = {1996},
  volume = {134},
  pages = {197--222},
  nremark = {orbit example}
}

@ARTICLE{GRAN96,
  author = {H. Granzier and M. Helmes and K. Trombitas},
  title = {Nonuniform elasticity of titin in cardiac myocytes: a study using
	immunoelectron microscopy and cellular mechanics},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {430--442}
}

@ARTICLE{GREA96,
  author = {M.L. Greaser and M.G. Sebestyen and J.D. Fritz and J.A. Wolff},
  title = {cDNA Sequence of Rabbit Cardiac Titin/Connectin},
  journal = {Adv. Biophys.},
  year = {1996},
  volume = {33},
  pages = {13--25}
}

@ARTICLE{GrJU96,
  author = {A. Griewank and D. Juedes and J. Utke.},
  title = {{ADOL-C}, a package for the automatic differentiation of algorithms
	written in {C}/{C\texttt{++}}},
  journal = ACMTMS,
  year = {1996},
  volume = {22},
  pages = {131--167},
  number = {2}
}

@ARTICLE{GRIG96,
  author = {N. Grigorieff and T.A. Ceska and K.H. Downing and J.M. Baldwin and
	R. Henderson},
  title = {Electron-crystallographic refinement of the structure of bacteriorhopsin},
  journal = {J. Mol. Biol.},
  year = {1996},
  volume = {259},
  pages = {393--421}
}

@ARTICLE{GRUB96,
  author = {Helmut Grubm{\"u}ller and Berthold Heymann and Paul Tavan},
  title = {Ligand Binding and Molecular Mechanics Calculation of the Streptavidin-Biotin
	Rupture Force},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {997--999}
}

@ARTICLE{GUAR96,
  author = {E. Gu{\`a}rdia and J. A. Padr{\'o}},
  title = {On the structure and dynamic properties of aqueous solutions: {Molecular}
	dynamics simulation of {Cl}$^{-}$ and {Cl}$^{2-}$ in water},
  journal = MS,
  year = {1996},
  volume = {17},
  pages = {83--94}
}

@ARTICLE{HACK96,
  author = {D.D. Hackney},
  title = {The kinetic cycles of myosin, kinesin, and dynein},
  journal = {Ann.\ Rev.\ Physiol.},
  year = {1996},
  volume = {58},
  pages = {731--750}
}

@ARTICLE{HACK96A,
  author = {D.D. Hackney},
  title = {Myosin and kinesin: mother and child reunited},
  journal = CHB,
  year = {1996},
  volume = {3},
  pages = {525--528}
}

@ARTICLE{HAGE96,
  author = {S. J. Hagen and J. Hofrichter and A. Szabo and W. A. Eaton},
  title = {Diffusion limited contact formation in unfolded cytochrome c: estimating
	the maximum rate of protein folding},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1996},
  volume = {93},
  pages = {11615--11617},
  number = {21}
}

@ARTICLE{Halg95,
  author = {T. A. Halgren},
  title = {The {M}erck Molecular Force Field: {I}. Basis, Form, Scope, Parameterization
	and Performance of {MMFF94}},
  journal = {J. Comput. Chem.},
  year = {1996}
}

@ARTICLE{HANE96,
  author = {S. Hanessian and P.V. Devasthale},
  title = {Design and Synthesis of Novel, Pseudo {C2} Symmetric Inhibitors of
	{HIV} Protease},
  journal = {Bioorg.\ Med.\ Chem.\ Lett.},
  year = {1996},
  volume = {6},
  pages = {2201--2206}
}

@ARTICLE{HaOE96,
  author = {Ulrich H. E. Hansmann and Yuko Okamoto and Frank Eisenmenger},
  title = {Molecular dynamics, {L}angevin and hybrid {M}onte {C}arlo simulations
	in a multicanonical ensemble},
  journal = {Chem. Phys. Lett.},
  year = {1996},
  volume = {259},
  pages = {321--330}
}

@ARTICLE{HARA96,
  author = {G. Haran and K. Wynne and C. C. Moser and P. L. Dutton and R. M.
	Hochstrasser},
  title = {Level Mixing and Energy Redistribution in Bacterial Photosynthetic
	Reaction Centers},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {5562--5569}
}

@ARTICLE{HASS96,
  author = {K.C. Hasson and Feng Gai and Philip A. Anfinrud},
  title = {{The photoisomerization of retinal in bacteriorhodopsin: Experimental
	evidence for a three-state model}},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {15124--15129}
}

@ARTICLE{ANFI96,
  author = {K.~C. Hasson and F. Gai and P.~A. Anfinrud},
  title = {The photoisomerization of retinal in bacteriorhopsin: experiment
	evidence for a three-state model},
  journal = PNAS,
  year = {1996},
  status = {submitted}
}

@ARTICLE{HEAT96,
  author = {Patrick J. Heath and James B. Clendenning and Brian S. Fujimoto and
	J. Michael Schurr},
  title = {Effect of Bending Strain on the Torsion Elastic Constant of {DNA}},
  journal = JMB,
  year = {1996},
  volume = {260},
  pages = {718--730}
}

@ARTICLE{HERS96,
  author = {H.R. Herschman},
  title = {{Prostaglandin synthase 2}},
  journal = BBA,
  year = {1996},
  volume = {1299},
  pages = {125--140}
}

@ARTICLE{HiLe96,
  author = {D. Hinds and M. Levitt},
  title = {From Structure to Sequence and Back Again},
  journal = {J. Mol. Biol.},
  year = {1996},
  volume = {258},
  pages = {201--209}
}

@ARTICLE{HIRO96,
  author = {N. Hirokawa},
  title = {Organelle transport along microtubules - the role of {KIF}s},
  journal = TCB,
  year = {1996},
  volume = {6},
  pages = {135--141}
}

@ARTICLE{HIRO96A,
  author = {K. Hirose and A. Lockhart and R.A. Cross and L.A. Amos},
  title = {Three-dimensional cryoelectron microscopy of dimeric kinesin and
	ncd motor domains on microtubules},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {9539--9544}
}

@ARTICLE{HOFM96,
  author = {E. Hofmann and P.M. Wrench and F.P. Sharples and R.G. Hiller and
	W. Welte and K. Diederichs},
  title = {Structural basis of light harvesting by carotenoids: peridinin-chlorophyll-protein
	from {{\em Amphidinium carterae}}},
  journal = SCI,
  year = {1996},
  volume = {272},
  pages = {1788--1791}
}

@ARTICLE{HoSa96,
  author = {L. Holm and C. Sander},
  title = {Mapping the Protein Universe},
  journal = SCI,
  year = {1996},
  volume = {273},
  pages = {595--603}
}

@ARTICLE{HOSL96,
  author = {Jonathan P. Hosler and James P. Shapleigh and D. M. Mitchell and
	Y. Kim and M. A. Pressler and C. Georgiou and G. T. Babcock and J.
	O. Alben and S. {Ferguson-Miller} and Robert B. Gennis},
  title = {Polar Residues in Helix {VIII} of Subunit {I} of Cytochrome c Oxidase
	Influence the Activity and the Structure of the Active Site.},
  journal = {Biochemistry},
  year = {1996},
  volume = {35},
  pages = {10776},
  number = {33},
  annote = {pdf}
}

@ARTICLE{HOWA96,
  author = {J. Howard},
  title = {The movement of kinesin along microtubules},
  journal = {Ann.\ Rev.\ Physiol.},
  year = {1996},
  volume = {58},
  pages = {703--729}
}

@INCOLLECTION{HU96,
  author = {Xiche Hu and Dong Xu and Kenneth Hamer and Klaus Schulten and J{\"u}rgen
	Koepke and Hartmut Michel},
  title = {Knowledge-Based Structure Prediction of the Light-Harvesting Complex
	{II} of {{\em Rhodospirillum molischianum}}},
  booktitle = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation
	and Protein Folding},
  publisher = AMS,
  year = {1996},
  editor = {P. M. Pardalos and D. Shalloway and G. Xue},
  pages = {97--122},
  address = {Providence, R.I.}
}

@INCOLLECTION{HU96A,
  author = {Xiche Hu and Dong Xu and Kenneth Hamer and Klaus Schulten and J{\"u}rgen
	Koepke and Hartmut Michel},
  title = {Prediction of the Structure of an Integral Membrane Protein--the
	Light-Harvesting Complex {II} of {{\em Rhodospirillum molischianum}}},
  booktitle = {Biological Membranes: A Molecular Perspective from Computation and
	Experiment},
  publisher = {Birkh\"auser},
  year = {1996},
  editor = {K.M. Merz and B. Roux},
  pages = {503--533},
  address = {Cambridge, MA}
}

@ARTICLE{HuKi96,
  author = {Gary A. Huber and Sangtae Kim},
  title = {Weighted-Ensemble {B}rownian Dynamics Simulations for Protein Association
	Reactions},
  journal = {Bioph.\ J.},
  year = {1996},
  volume = {70},
  pages = {97--110}
}

@ARTICLE{HuNe96,
  author = {Koji Hukushima and Koji Nemoto},
  title = {Exchange {M}onte {C}arlo Method and Application to Spin Glass Simulations},
  journal = {J. Phys. Soc. of Japan},
  year = {1996},
  volume = {65},
  pages = {1604--1608},
  number = {6}
}

@ARTICLE{HLLW96,
  author = {W. Humphrey and H. Lu and I. logunov and H.-J. Werner and K. Schulten},
  title = {Three electronic state model of the primary phototransformation of
	bacteriorhodopsin},
  journal = PNAS,
  year = {1996},
  status = {submitted}
}

@ARTICLE{HuDS96,
  author = {William F. Humphrey and Andrew Dalke and Klaus Schulten},
  title = {{VMD} -- {V}isual {M}olecular {D}ynamics},
  journal = JMG,
  year = {1996},
  volume = {14},
  pages = {33--38}
}

@ARTICLE{IMPR96,
  author = {Sabina Improta and Anastasia Politou and Annalisa Pastore},
  title = {Immunoglobulin-like modules from titin {I}-band: extensible components
	of muscle elasticity},
  journal = STR,
  year = {1996},
  volume = {4},
  pages = {323--337}
}

@ARTICLE{IWAT96,
  author = {So Iwata and Monica Saynovits and Thomas A. Link and Hartmut Michel},
  title = {Structure of a Water Soluble Fragment of the '{R}ieske' Iron-Sulphur
	Protein of the Bovine Heart Mitochondrial Cytochrome $bc_1$ Complex
	Determined by {MAD} Phasing at 1.5~\AA\ resolution},
  journal = STR,
  year = {1996},
  volume = {4},
  pages = {567--579}
}

@ARTICLE{JAYA96,
  author = {B.~Jayaram and D.~Beveridge},
  title = {Modelling {DNA} in Aqueous Solutions -- Theoretical and Computer
	Simulation Studies on the Ion Atmosphere of {DNA}},
  journal = ARBBS,
  year = {1996},
  volume = {25},
  pages = {367--394}
}

@ARTICLE{JiGl96,
  author = {Y. Jiang and J.~A. Glazier},
  title = {Modeling Biomaterials},
  journal = { \small \texttt{http://www.nd.edu/\~{}jglazier/papers/Yi\_review\_2001/Yi\_review\_2001.pdf}},
  year = {1996},
  volume = {preprint}
}

@ARTICLE{JIME96,
  author = {R. Jimenez and S. Dikshit and S. Bradforth and G. Fleming},
  title = {Electronic Excitation Transfer in the LH2 Complex of {\em Rhodobacter
	sph aeroides}},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {6825--6834}
}

@ARTICLE{JONA96,
  author = {D. M. Jonas and M. J. Lang and Y. Nagasawa and T. Joo and G. R. Fleming},
  title = {Pump-Probe Polarization Anisotropy Study of Femtosecond Energy Transfer
	within the Photosynthetic Reaction Center of {\em Rhodobacter sphaeroides}
	R26},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {12660--12673}
}

@ARTICLE{JOO96,
  author = {T. Joo and Y. Jia and J.-Y. Yu and D.M. Jonas and G.R. Fleming},
  title = {Dynamics in isolated bacterial light harvesting antenna ({LH2}) of
	{\em Rhodobacter sphaeroides} at room temperature},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {2399--2409}
}

@ARTICLE{JORG96,
  author = {J.S. Jorgensen and J.B. Pederen and A.I. Shushin},
  title = {Magnetic field dependent yield of geminate radical pair recombination
	in micells. Effect of intraradical spin lattice relaxation},
  journal = {Chem.\~Phys.},
  year = {1996},
  volume = {211},
  pages = {235--248}
}

@ARTICLE{JUDE96,
  author = {C.~Judelson and M.~L.~Privalsky},
  title = {{DNA} recognition by normal and oncogenic thyroid hormone receptors
	-- unexpected diversity in half-site specificity controlled by non--zinc-finger
	determinants.},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {10800--10805},
  annote = {on the web}
}

@ARTICLE{JUNG96,
  author = {P. Jungwirth and R.B. Gerber},
  title = {Quantum dynamics simulations of nonadiabatic processes in many-atom
	systems: Photoexcited {Ba(Ar)10} and {Ba(Ar)20} clusters},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {104},
  pages = {5803}
}

@ARTICLE{JAHN96,
  author = {Fritz J{\"a}hnig},
  title = {What is the surface tension of a lipid bilayer membrane?},
  journal = BJ,
  year = {1996},
  volume = {71},
  pages = {1348--1349}
}

@ARTICLE{KATZ96,
  author = {J.~A.~Katzenellenbogen and B.~W.~O'Malley and B.~S.~Katzenellenbogen},
  title = {Tripartite steroid hormone receptor pharmacology: Interaction with
	multiple effector sites as a basis for the cell-- and promoter--specific
	action of these hormones.},
  journal = MEC,
  year = {1996},
  volume = {10},
  pages = {119--131},
  annote = {in press}
}

@ARTICLE{KELL96,
  author = {M. Kellermayer and H. Granzier},
  title = {Elastic Properties of single titin molecules made visible through
	fluorescent {F}-actin binding},
  journal = BBRC,
  year = {1996},
  volume = {221},
  pages = {491--497}
}

@ARTICLE{KEMP96,
  author = {AD Kennedy and R Edwards and H Mino and B Pendleton},
  title = {Tuning the generalized {H}ybrid {M}onte {C}arlo algorithm},
  journal = {Nuclear Physics B},
  year = {1996},
  pages = {781--784}
}

@ARTICLE{KENN96,
  author = {J.T.M. Kennis and A.M. Streltsov and T.J. Aartsma and T. Nozawa and
	J. Amesz},
  title = {Energy Transfer and Exciton Coupling in Isolated {B}800-850 Complexes
	of the Photosynthetic Purple Sulfur Bacterium Chromatium Tepidum
	- the Effect of Structural Symmetry on Bacteriochlorophyll Excited
	States},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {2438--2442}
}

@ARTICLE{KERF96,
  author = {C. Kerfeld and H. Anwar and R. Interrante and S. Merchant and T.
	Yeates},
  title = {The structure of chloroplast cytochrome c6 at 1.9 angstroms resolution:
	evidence for functional oligomerization},
  journal = JMB,
  year = {1996},
  volume = {250},
  pages = {627}
}

@MISC{KIMU96,
  author = {Y. Kimura},
  title = {Lecture at the 7the International Conference on Retinal Proteins},
  howpublished = {Zichron Yaakov, Israel},
  year = {1996}
}

@ARTICLE{KBHB96,
  author = {P. D. Kirchhoff and M. B. Bass and B. A. Hanks and J.M. Briggs and
	A. Collet and J. A. McCammon},
  title = {Structural Fluctuations of a Cryptophane Host: A Molecular Dynamics
	Simulation},
  journal = JACS,
  year = {1996},
  volume = {118},
  pages = {3237--3246}
}

@ARTICLE{KIRS96,
  author = {J.L. Kirschvink},
  title = {A possible mechanism for coupling nonthermal levels of radiation
	to biological systems},
  journal = {Bioelectromag.},
  year = {1996},
  volume = {17},
  pages = {242--245}
}

@ARTICLE{KOEP96,
  author = {J{\"u}rgen Koepke and Xiche Hu and Cornelia M{\"u}nke and Klaus Schulten
	and Hartmut Michel},
  title = {The Crystal Structure of the Light Harvesting Complex {II} {(B800-850)}
	from {{\em Rhodospirillum molischianum}}.},
  journal = {Structure},
  year = {1996},
  volume = {4},
  pages = {581--597},
  techrep = {TB-96-02}
}

@ARTICLE{Kora96,
  author = {Holly Korab},
  title = {Modeling Hierarchies---Doing More with Less: Interview with {B}ill
	{G}oddard},
  journal = {NCSA Access},
  year = {1996},
  volume = {10},
  pages = {4--5},
  number = {1}
}

@ARTICLE{Koretke96,
  author = {K K Koretke and Z Luthey-Schulten and P G Wolynes},
  title = {Self-consistently optimized statistical mechanical energy functions
	for sequence structure alignment},
  journal = {Protein Science},
  year = {1996},
  volume = {5},
  pages = {1043--1059}
}

@ARTICLE{KOSZ96,
  author = {Ioan Kosztin and Byron Faber and Klaus Schulten},
  title = {Introduction to the Diffusion {M}onte {C}arlo Method},
  journal = AJP,
  year = {1996},
  volume = {64},
  pages = {633--644},
  annote = {submitted on 2/14/95}
}

@ARTICLE{KOUT66,
  author = {J. Koutecky},
  title = {Contribution to the Theory of Alternant Systems},
  journal = JCP,
  year = {1996},
  volume = {44},
  pages = {3702--3706}
}

@ARTICLE{KOYA96,
  author = {Y. Koyama and M. Kuki and P.O. Andersson and T. Gillbro},
  title = {Singlet excited states and the light-harvesting function of carotenoids
	in bacterial photosynthesis},
  journal = PCPB,
  year = {1996},
  volume = {63},
  pages = {243--256}
}

@ARTICLE{KRAU96,
  author = {Norbert Krau{\ss} and Wolf-Dieter\ Schubert and Olaf Klukas and Petra
	Fromme and Horst T.\ Witt and Wolfram Saenger},
  title = {Photosystem {I} at 4 {{\AA}} Resolution Represents the First Structural
	Model of a Joint Photosynthetic Reaction Centre and Core Antenna
	System},
  journal = NATSB,
  year = {1996},
  volume = {3},
  pages = {965--973},
  number = {11}
}

@ARTICLE{KULL96,
  author = {F. Jon Kull and Elena P. Sablin and Rebecca Lau and Robert J. Fletterick
	and Ronald D. Vale},
  title = {Crystal structure of the kinesin motor domain reveals a structural
	similarity to myosin},
  journal = NAT,
  year = {1996},
  volume = {380},
  pages = {550--555}
}

@ARTICLE{KURU96,
  author = {Ravi G. Kurumbail and Anna M. Stevens and James K. Gierse and Joseph
	J. McDonald and Roderick A. Stegeman and Jina Y. Pak and Daniel Gildehaus
	and Julie M. Miyashiro and Thomas D. Penning and Karen Seibert and
	Peter C. Isakson and William C. Stallings},
  title = {{Structural basis for selective inhibition of cyclooxygenase-2 by
	anti-inflammatory agents}},
  journal = NAT,
  year = {1996},
  volume = {348},
  pages = {644--648},
  number = {6610}
}

@ARTICLE{LAID96,
  author = {K. E. Laidig and V. Daggett},
  title = {Testing the Modified Hydration-Shell Hydrogen-Bond Model of Hydrophobic
	Effects Using Molecular Dynamics Simulation},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {5616--5619}
}

@ARTICLE{LAM96,
  author = {P.~Y.~Lam and Y.~Pu and P.~K.~Jadhav and P.~E.~Aldrich and G.~V.~DeLucca
	and C.~J.~Eyerman and C.~H.~Chang and G.~Emmett and E.~R.~Holler
	and W.~F.~Daneker and L.~Li and P.~N.~Confalone and R.~J.~McHugh
	and Q.~Han and R.~Li and J.~A.~Markwalder and S.~P.~Seitz and T.~R.~Sharpe
	and L.~T.~Bacheler and M.~M.~Rayner and R.~M.~Klabe and L.~Shum and
	D.~L.~Winslow and D.~M.~Kornhauser and C.~N.~Hodge {it et al.}.},
  title = {Cyclic {HIV} protease inhibitors: synthesis, conformational analysis,
	{P2\/P2'} structure-activity relationship, and molecular recognition
	of cyclic ureas},
  journal = JMC,
  year = {1996},
  volume = {39},
  pages = {3514--3525}
}

@ARTICLE{LaDB96,
  author = {C.~G. Lambert and T.~A. Darden and J.~A. Board},
  title = {A Multipole-Based Algorithm for Efficient Calculation of Forces and
	Potentials in Macroscopic Periodic Assemblies of Particles},
  journal = JCMP,
  year = {1996},
  volume = {126},
  pages = {274--287},
  number = {2}
}

@ARTICLE{LAW96,
  author = {C.K. Law and R.S. Knox and J.H. Eberly},
  title = {Time-resolved fluorescence anisotropy in degenerate two-state systems:
	the role of complex stochastic processes},
  journal = {Chem.~Phys.~Lett.},
  year = {1996},
  volume = {258},
  pages = {352--355}
}

@ARTICLE{LEAH96,
  author = {D.~J. Leahy and I. Aukhil and H. P. Erickson},
  title = {2.0 {\AA}~crystal structure of a four-domain segment of human fibronectin
	encompassing the {R}{G}{D} loop and synergy region.},
  journal = {Cell},
  year = {1996},
  volume = {84},
  pages = {155--164}
}

@ARTICLE{LEBO96,
  author = {F. Lebon and C. Vinals and E. Feytmans and F. Durant},
  title = {Computational Drug Design of New {HIV}-1 Protease Inhibitors},
  journal = APB,
  year = {1996},
  volume = {104},
  pages = {B44}
}

@ARTICLE{LEEC96,
  author = {J. Leech and J. Prins and J. Hermans},
  title = {{S}{M}{D}: Visual Steering of Molecular Dynamics for Protein Design},
  journal = IEEECSE,
  year = {1996},
  volume = {3},
  pages = {38--45},
  number = {4}
}

@INCOLLECTION{LeRS96,
  author = {Benedict J. Leimkuhler and S. Reich and R.~D. Skeel},
  title = {Integration methods for molecular dynamics},
  booktitle = {Mathematical Approaches to Biomolecular Structure and Dynamics},
  publisher = {Springer-Verlag},
  year = {1996},
  editor = {Jill P. Mesirov and Klaus Schulten and De Witt Sumners},
  volume = {82},
  series = {IMA Volumes in Mathematics and its Applications},
  pages = {161--185}
}

@ARTICLE{LESK96,
  author = {A. M. Lesk and W. D. Fordham},
  title = {Conservation and Variability in the Structures of Serine Proteinases
	of the Chymotrypsin Family},
  journal = JMB,
  year = {1996},
  volume = {258},
  pages = {501--537}
}

@ARTICLE{LEUP96,
  author = {D. Leupold and H. Stiel and K. Teuchner and F. Nowak and W. Sandner
	and B. Ucker and H. Scheer},
  title = {Size Enhancement of Transition Dipoles to One and Two-exciton Bands
	in a Photosynthetic Antenna},
  journal = PRL,
  year = {1996},
  volume = {77},
  pages = {4675--4678}
}

@ARTICLE{LATT96,
  author = {H.\ Levine and I.\ Aranson and L.\ Tsimring and T. V. Truong},
  title = {Positive genetic feedback governs cAMP spiral wave formation in dictyostelium},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {6382}
}

@ARTICLE{LEWI96,
  author = {Mitchell Lewis and Geoffrey Chang and Nancy C. Horton and Michele
	A. Kercher and Helen C. Pace and Maria A. Schumacher and Richard
	G. Brennan and Ponzy Lu},
  title = {Crystal structure of the lactose operon repressor and its complexes
	with {DNA} and inducer},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {1247--1254}
}

@ARTICLE{LI96,
  author = {Leping Li and Tom Darden and Richard Hiskey and Lee Pedersen},
  title = {Homology modeling and molecular dynamics simulations of the {Gla}
	domains of human coagulation factor {IX} and its {G[12]A} mutant},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {2475--2479}
}

@ARTICLE{LINK96,
  author = {T. A. Link},
  title = {The role of the ``{R}ieske'' iron sulfur protein in the hydroquinone
	oxidation ({Q}$_{p-}$) site of the cytochrome $bc_1$ complex: {T}he
	"proton-gated affinity change" mechanism.},
  journal = FEBS,
  year = {1996},
  volume = {412},
  pages = {257--264}
}

@ARTICLE{LOGU96,
  author = {Ilya Logunov and Klaus Schulten},
  title = {Quantum Chemistry -- Molecular Dynamics Study of the Dark Adaptation
	Process in Bacteriorhodopsin},
  journal = JACS,
  year = {1996},
  volume = {118},
  pages = {9727--9735},
  techrep = {TB-95-23}
}

@ARTICLE{LOGU96B,
  author = {S. Logunov and M. El-Sayed and J. Lanyi},
  title = {Replacement Effects of Neutral Amino Acid Residues of Different Molecular
	Volumes in the Retinal Binding Cavity of Bacteriorhodopsin on the
	Dynamics of its Primary Process},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {2875--2881}
}

@ARTICLE{LOGU96A,
  author = {S. Logunov and M. El-Sayed and L. Song},
  title = {Photoisomerization Quantum Yield and Apparent Energy Content of the
	{K} Intermediate in the Photocycles of Bacteriorhodopsin, its Mutants
	{D85N}, {R82Q}, and {D212N}, and Deionized Blue Bacteriorhodopsin},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {2391--2398}
}

@ARTICLE{LOUI96,
  author = {S.~Louise-May and P.~ Auffinger and E.~Westhof.},
  title = {Calculations of nucleic acid conformations},
  journal = COSB,
  year = {1996},
  volume = {6},
  pages = {289--298},
  annote = {review article on DNA solution structures and hydration patterns}
}

@ARTICLE{LUND96,
  author = {T.~Lundb{\"a}ck and T.~H{\"a}rd},
  title = {Sequence --specific {DNA}--binding dominated by dehydration.},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {4754--4759},
  annote = {removal of a methyl group at the dna-protein interface is equivalent
	with a replacement by an ordered water molecule}
}

@ARTICLE{LUON96,
  author = {Chrisine Luong and Aaron Miller and Jim Barnett and Joan Chow and
	Chakk Ramesha and Michelle F. Browner},
  title = {{Flexibility of the NSAID binding site in the structure of human
	cyclooxygenase-2}},
  journal = NATSB,
  year = {1996},
  volume = {3},
  pages = {927--933},
  number = {11}
}

@ARTICLE{LuGu96,
  author = {Brock A. Luty and Wilfred F. van Gusteren},
  title = {Calculating Electrostatics Interactions Using the Particle--Particle
	Particle--Mesh Method with Nonperiodic Long-Range Interactions},
  journal = {J.~Phys.\ Chem.},
  year = {1996},
  volume = {100},
  pages = {2581--2587},
  nremark = {new treatment of nonperiodic boundaries}
}

@BOOK{LUTZ96,
  title = {Programming {P}ython: Object-Oriented Scripting},
  publisher = {O'Reilly \& Assoc},
  year = {1996},
  author = {Mark Lutz}
}

@ARTICLE{LoSD9x,
  author = {M. L{\'o}pez-Marcos and J. M. Sanz-Serna and J. C. D\'iaz},
  title = {Are Gauss-Legendre Methods Useful in Molecular Dynamics?},
  journal = {J. Comput.\ Appl.\ Math.},
  year = {1996},
  volume = {67},
  pages = {173--179}
}

@INPROCEEDINGS{LoSS96a,
  author = {M. L{\'o}pez-Marcos and J. M. Sanz-Serna and R.~D. Skeel},
  title = {Cheap Enhancement of Symplectic Integrators},
  booktitle = {Numerical Analysis 1995},
  year = {1996},
  editor = {D. F. Griffiths and G. A. Watson},
  pages = {107--122},
  address = {London},
  publisher = {Longman Group},
  nack = {Iber, doensf, nsfarpa, nih},
  nrights = {to include in other volumes of our own work}
}

@ARTICLE{MAHA96,
  author = {L. Mahadevan and J. B. Keller},
  title = {Coiling of flexible rods},
  journal = PRSLA,
  year = {1996},
  volume = {452},
  pages = {1679--1694}
}

@ARTICLE{MAKR96,
  author = {N. Makri and E Sim and D.E. Makarov and M. Topaler},
  title = {Long-time quantum simulation of the primary charge separation in
	bacterial photosynthesis},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {3926--3931}
}

@ARTICLE{MANN96,
  author = {Robert S. Manning and John H. Maddocks and Jason D. Kahn},
  title = {A continuum rod model of sequence-dependent {DNA} structure},
  journal = JCP,
  year = {1996},
  volume = {105},
  pages = {5626--5646},
  number = {13}
}

@ARTICLE{MTTK96,
  author = {Glenn J. Martyna and Mark E. Tuckerman and Douglas J. Tobias and
	Michael L. Klein},
  title = {Explicit Reversible Integrators for Extended System Dynamics},
  journal = {Mol.\ Phys.},
  year = {1996},
  volume = {87},
  pages = {1117--1157},
  number = {5},
  nabstract = {Explicit reversible integrators, suitable for use in large-scale computer
	simulations, are derived for extended systems generating the canonical
	and isothermal-isobaric ensembles. The new methods are compared with
	the standard implicit (iterative) integrators on some illustrative
	example problems. In addition, modification of the proposed algorithms
	for multiple time step integration is outlined.}
}

@ARTICLE{MASF96,
  author = {J.L. Masferrer and P.C. Isakson and K. Seibert},
  title = {{Cyclooxygenase-2 Inhibitors}},
  journal = {NSAIDs, Eicosanoids, and the Gastroenteric Tract},
  year = {1996},
  volume = {25},
  pages = {363--372},
  number = {2}
}

@ARTICLE{MaTa96,
  author = {L. R. Matheson and R. E. Tarjan},
  title = {Parallelism in Multigrid Methods: How Much Is Too Much?},
  journal = {International J. of Parallel Programming},
  year = {1996},
  volume = {24},
  pages = {397--432},
  number = {5}
}

@ARTICLE{MATT96,
  author = {Kathleen S. Matthews},
  title = {The whole lactose repressor},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {1245--1246}
}

@ARTICLE{MCGI96,
  author = {Pete McGill and Mark F. Schumaker},
  title = {Boundary conditions for single-ion diffusion},
  journal = BJ,
  year = {1996},
  volume = {71},
  pages = {1723--1742},
  annote = {Applies experimental ion flux data to Roux's gramadicin PMF results}
}

@ARTICLE{ARNV96,
  author = {K. Arnvig McGuire and W. S. Davidson and A. Jonas},
  title = {High Yield Overexpression and Characterization of Human Recombinant
	Proapolipoprotein {A-I}},
  journal = JLR,
  year = {1996},
  volume = {37},
  pages = {1519}
}

@ARTICLE{MeOt96,
  author = {M. Melchior and H.C. {{\"O}ttinger}},
  title = {Variance Reduced Simulations of Polymer Dynamics},
  journal = {J.Chem.\ Phys.},
  year = {1996},
  volume = {105},
  pages = {3316--3331},
  number = {8},
  annote = {Review on the variance reduced simulations.}
}

@ARTICLE{MELK96,
  author = {R. Melki and S. Fievez and M.-F. Carlier},
  title = {Continuous Monitoring of {P}$_i$ Release Following Nucleotide Hydrolysis
	in Actin or Tubulin Using 2-Amino-6-mercapto-7-methylpurine Ribonucleoside
	and Purine-Nucleoside Phosphorylase as an Enzyme-Linked Assay},
  journal = BCH,
  year = {1996},
  volume = {35},
  pages = {12038--12045}
}

@ARTICLE{MiSc96,
  author = {Bimal Mishra and Tamar Schlick},
  title = {The Notion of Error in {L}angevin Dynamics: 1. {L}inear Analysis},
  journal = {J.Chem.\ Phys.},
  year = {1996},
  volume = {105},
  pages = {299--318}
}

@ARTICLE{MITC96B,
  author = {David M. Mitchell and Fetter, John R. and Gennis, Robert B.},
  title = {Site-Directed Mutagenesis of Residues Lining a Putative Proton Transfer
	Pathway in Cytochrome c Oxidase from {\em {Rhodobacter sphaeroides}}.},
  journal = {Biochemistry},
  year = {1996},
  volume = {35},
  pages = {13089},
  number = {40},
  annote = {copy+pdf}
}

@ARTICLE{MODI96,
  author = {S. Modi and M. J. Paine and M. J. Sutcliffe and L.-Y. Lian and W.
	U. Primrose and C. R. Wolf and G. C. K. Roberts},
  title = {A model for human cytochrome {$P_{450}$ 2D6} based on homology modeling
	and {NMR} studies of substrate binding},
  journal = BCH,
  year = {1996},
  volume = {35},
  pages = {4540--4550}
}

@ARTICLE{MoGl96,
  author = {J. C. M. Mombach and J.A. Glazier},
  title = {Single cell motion in aggregates of embryonic cells},
  journal = {Phys. Rev. Lett.},
  year = {1996},
  volume = {76},
  pages = {3032--3035},
  number = {16}
}

@ARTICLE{MONS96a,
  author = {R. Monshouwer and R. {van Grondelle}},
  title = {Excitations and excitons in bacterial light-harvesting complexes},
  journal = {Biochim. Biophys. Acta},
  year = {1996},
  volume = {1275},
  pages = {70--75}
}

@ARTICLE{MONS96,
  author = {R. Monshouwer and R. van Grondelle},
  title = {Excitations and Excitons in Bacterial Light-harvesting Complexes},
  journal = {Biochim. et Biophys. Acta-Bioenergetics},
  year = {1996},
  volume = {1275},
  pages = {70--75}
}

@ARTICLE{NAGA96A,
  author = {H. Nagae},
  title = {Theory of solvent effects on electronic absorption spectra of rodlike
	or disklike solute molecules: frequency shifts},
  journal = JCP,
  year = {1996},
  volume = {106},
  pages = {5159--5170}
}

@ARTICLE{NAGA96,
  author = {Bhushan Nagar and Michael Overdulin and Mitsuhiko Ikura and James
	Rini},
  title = {Structural basis of calcium-induced {E}-cadherin rigidification and
	dimerization},
  journal = NAT,
  year = {1996},
  volume = {380},
  pages = {360--364}
}

@ARTICLE{NARD96,
  author = {A.~M.~Nardulli and L.~E.~Romine and C.~Carpo and G.~L.~Greene and
	B.~Rainish},
  title = {Estrogen receptor affinity and location of consensus and imperfect
	estrogen response elements influence transcription activation of
	simplified promoters.},
  journal = MEC,
  year = {1996},
  volume = {10},
  pages = {694--704}
}

@ARTICLE{Neal96,
  author = {R. M. Neal},
  title = {Sampling from Multimodal Distributions Using Tempered Transitions},
  journal = {Statistics and Computing},
  year = {1996},
  volume = {6},
  pages = {353--366}
}

@BOOK{Neal96b,
  title = {Bayesian Learning for Neural Networks},
  publisher = {Springer-Verlag},
  year = {1996},
  author = {Radford M. Neal},
  volume = {118},
  series = {Lecture Notes in Statistics},
  address = {New York},
  abstract = {Artificial "neural networks" are widely used as flexible models for
	classification and regression applications, but questions remain
	about how the power of these models can be safely exploited when
	training data is limited. This book demonstrates how Bayesian methods
	allow complex neural network models to be used without fear of the
	"overfitting" that can occur with traditional training methods. Insight
	into the nature of these complex Bayesian models is provided by a
	theoretical investigation of the priors over functions that underlie
	them. A practical implementation of Bayesian neural network learning
	using Markov chain {M}onte {C}arlo methods is also described, and
	software for it is freely available over the Internet. Presupposing
	only basic knowledge of probability and statistics, this book should
	be of interest to researchers in statistics, engineering, and artificial
	intelligence.}
}

@ARTICLE{NELS96,
  author = {M. Nelson and W. Humphrey and A. Gursoy and A. Dalke and L. Kal{\'e}
	and R.~D. Skeel and K. Schulten},
  title = {{NAMD} -- {A} Parallel, Object-Oriented Molecular Dynamics Program},
  journal = JSCA,
  year = {1996},
  volume = {10},
  pages = {251--268},
  number = {4},
  readme = {[Beckman Institute Technical Report TB-95-17]}
}

@ARTICLE{NOVO96,
  author = {V. I. Novoderezhkin and A. P. Razjivin},
  title = {The theory of Forster-type migration between clusters of strongly
	interacting molecules: application to light-harvesting complexes
	of purple bacteria},
  journal = CP,
  year = {1996},
  volume = {211},
  pages = {203--214}
}

@ARTICLE{OBST96,
  author = {S. Obst and H. Bradaczek},
  title = {Molecular Dynamics Study of the Structure and Dynamics of the Hydration
	Shell of Alkaline and Alkaline-Earth Metal Cations},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {15677--15687}
}

@ARTICLE{OLEN96,
  author = {Roberto Olender and Ron Elber},
  title = {Calculation of classical trajectories with a very large time step:
	{F}ormalism and numerical examples},
  journal = JCP,
  year = {1996},
  volume = {105},
  pages = {9299--9315},
  number = {20}
}

@ARTICLE{OLSO96,
  author = {W.~K.~Olson},
  title = {Simulating {DNA} at low resolution},
  journal = COSB,
  year = {1996},
  volume = {6},
  pages = {242--256}
}

@ARTICLE{PANC96,
  author = {A. R. Panchenko and Z. A. Luthey-Schulten and P. G. Wolynes},
  title = {Foldons, Protein Structural Modules and Exons},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {2008--2013}
}

@ARTICLE{PAPP96,
  author = {Rohit V. Pappu and William J. Schneller and David L. Weaver},
  title = {Electrostatic Multipole Representation of a Polypeptide Chain: An
	Algorithm for Simulation of Polypeptide Properties},
  journal = JCC,
  year = {1996},
  volume = {17},
  pages = {1033--1055},
  number = {8}
}

@ARTICLE{PARK96A,
  author = {Gary Parkinson and Angelo Gunasekera and J. Vojtechovsky and X. Zhang
	and T. A. Kunkel and Helen M. Berman and Richard E. Ebright},
  title = {Aromatic hydrogen bond in sequence-specific protein-{DNA} recognition},
  journal = NATSB,
  year = {1996},
  volume = {3},
  pages = {837--841},
  number = {10}
}

@ARTICLE{PARK96,
  author = {Gary Parkinson and Christofer Wilson and Angelo Gunasekera and Yon
	W. Ebright and Richard E. Ebright and Helen M. Berman},
  title = {Structure of the {CAP-DNA} complex at {2.5\,\AA} resolution: {A}
	complete picture of the protein-{DNA} interface},
  journal = PNAS,
  year = {1996},
  volume = {260},
  pages = {395--408}
}

@ARTICLE{PASC96,
  author = {T. Pascher and J. P. Chesick and J. R. Winkler and H. B. Gray},
  title = {Protein Folding Triggered by Electron Transfer},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {1558--1560}
}

@ARTICLE{PATT96,
  author = {P.A. Patten and N.S. Gray and P.L. Yang and C.B. Marks and G.J. Wedemayer
	and J.J. Boniface and R.C. Stevens and P.G. Schultz},
  title = {The Immunological Evolution of Catalysis},
  journal = {Science},
  year = {1996},
  volume = {271},
  pages = {1086--1091}
}

@ARTICLE{PeMo96,
  author = {J. T. Pedersen and J. Moult},
  title = {Genetic Algorithms for Protein Structure Prediction},
  journal = {Curr. Opin. Struct. Biol.},
  year = {1996},
  volume = {6},
  pages = {227--231}
}

@ARTICLE{PELL96,
  author = {Matteo Pellegrini and Niels Gr{\o}nbech-Jensen and Sebastian Doniach},
  title = {Potentials of mean force for biomolecular simulations: Theory and
	test on alanin dipeptide},
  journal = JCP,
  year = {1996},
  volume = {104},
  pages = {8639--8648},
  number = {21}
}

@ARTICLE{PERR96,
  author = {Manoussos Perros and Thomas A. Steitz and Michael G. Fried and J.
	Michael Hudson},
  title = {{DNA} looping and {{\it Lac} repressor-CAP} interaction},
  journal = SCI,
  year = {1996},
  volume = {274},
  pages = {1929--1931},
  annote = {this is a technical comment}
}

@ARTICLE{OTF96,
  author = {E.F. Pettersen and G.S. Couch and C.C. Huang and T.E. Ferrin},
  title = {The Object Technology Framework: An Object-Oriented Interface to
	Molecular Data},
  journal = {Information Systems},
  year = {1996},
  status = {submitted}
}

@ARTICLE{PETZ96,
  author = {L.~N.~Petz and A.~M.~Nardulli and J.~Kim and K.~B.~Horwitz and L.~P.~Freedman
	and D.~J.~Shapiro},
  title = {{DNA} Bending is Induced by Binding of the Glucocorticoid Receptor
	{DNA} Binding Domain and the Progesterone Receptors to their Response
	Element},
  year = {1996},
  note = {Submitted}
}

@ARTICLE{PlHe96,
  author = {S. Plimpton and B. Hendrickson},
  title = {A New Parallel Method for Molecular Dynamics Simulation of Macromolecular
	Systems},
  journal = JCC,
  year = {1996},
  volume = {17},
  pages = {326},
  number = {3},
  nremark = {force parallelism, partition the ``force matrix'' into blocks and
	compute each block concurrently, B. B. says this is the most scalable
	approach, also 1994 tech rept, Sandia, Parallel Computational Sciences
	Department 1421, MS 1111, Sandia National Laboratories, Albuquerque,
	NM 87185-1111. Phone: (505) 845-7873. E-Mail: sjplimp@zcs.sandia.gov}
}

@ARTICLE{POLA96,
  author = {K.~J.~Polach and J.~Widom},
  title = {A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins
	to Nucleosomal Target Sites},
  journal = JMB,
  year = {1996},
  volume = {258},
  pages = {800--812}
}

@ARTICLE{POLI96,
  author = {A. S. Politou and M. Gautel and S. Improta and L. Vangelista and
	A. Pastore},
  title = {The elastic {I}-band region of titin is assembled in a ``modular''
	fashion by weakly interacting {I}g-like domains},
  journal = JMB,
  year = {1996},
  volume = {255},
  pages = {604--616}
}

@ARTICLE{PoGl96,
  author = {E.~L. Pollock and J. Glosli},
  title = {Comments on {PPPM}, {FMM}, and the {E}wald Method for Large Periodic
	{C}oulombic systems},
  journal = CPC,
  year = {1996},
  volume = {95},
  pages = {93--110},
  annote = {Prompted by the need to simulate large molecular or gravitational
	systems and the availability of multiprocessor computers, alternatives
	to the standard Ewald calculation of Coulombic interactions have
	been developed. The two most popular alternatives, the fast multipole
	method (FMM) and the particle-particle particle-mesh (P3M) method
	are compared here to the Ewald method for a single processor machine.
	Parallel processor implementations of the P3M and Ewald methods are
	compared. The P3M method is found to be both faster than the FMM
	and easier to implement efficiently as it relies on commonly available
	software (FFT subroutines). Both the Ewald and P3M method are easily
	implemented on parallel architectures with the P3M method the clear
	choice for large systems.}
}

@ARTICLE{PrMa96,
  author = {Piero Procacci and Massimo Marchi},
  title = {Taming the {E}wald Sum in Molecular Dynamics Simulations of Solvated
	Proteins Via a Multiple Time Step Algorithm},
  journal = {J. Chem.\ Phys.},
  year = {1996},
  volume = {104},
  pages = {3003--3012},
  number = {8},
  nabstract = {Long range electrostatic forces are involved at a fundamental level
	in many biological phenomena. Their prohibitive computational costs
	often prevents their correct calculation in molecular dynamics (MD)
	simulations of biological molecules. In this paper we present a method
	to handle efficiently and exactly electrostatic interactions in MD
	simulations with periodic boundary conditions. Our scheme employs
	a multiple time step r-RESPA integration algorithm in combination
	with the Ewald summation technique, and is specifically targeted
	to simulation of large size complex molecular systems such as solvated
	proteins. In this approach, the force associated with each particle
	of the system is partitioned into four components which evolve in
	time with distinct and increasingly longer time scales. We found
	that a suitable time scale separation is achieved by subdividing
	the direct space nonbonded interactions, inclusive of Coulombic and
	van der Waals contributions, in a short, medium and long range shells.
	The fastest bonded forces are associated to the component with the
	shortest timescale, while the reciprocal space nonbonded interaction
	is included with the medium range direct space forces. Our method
	is general. It can be straightforwardly implemented for any biomolecular
	force fields used in condensed phase simulations and can be applied
	to other complex molecular systems such as molecular liquids and
	heterogeneous solutions (e.g., micelles, membranes, etc.). We carried
	out tests on solvated proteins samples containing 7 040 and 20 627
	atoms. Due to the nonlinear scaling of the Ewald computational cost
	with system size, the performance of our r-RESPA algorithm with respect
	to single time step algorithms with bond constraints grows with the
	number of particles. We reach a relative speed-up of 4.2 for a system
	composed of a solvated photosynthetic reaction center. (C) 1996 American
	Institute of Physics.}
}

@ARTICLE{PULL96,
  author = {T. Pullerits and M. Chachisvillis and V. Sundstrom},
  title = {Exciton Delocalization Length in the {B}850 Antenna of {{\em Rhodobacter
	sphaeroides}}},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {10787}
}

@ARTICLE{PULL96a,
  author = {T. Pullerits and V. Sundstrom},
  title = {Photosynthetic Light-Harvesting Pigment-protein Complexes: Toward
	Understanding How and Why},
  journal = ACR,
  year = {1996},
  volume = {29},
  pages = {381--389}
}

@ARTICLE{VANR96,
  author = {Mark J. van Raaij and Jan Pieter Abrahams and Andrew G.W. Leslie
	and John E. Walker},
  title = {The structure of the bovine F$_1$-ATPase complexed with the antibiotic
	inhibitor aurovertin B},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {6913--6917}
}

@ARTICLE{Raho96,
  author = {Jussi Rahola},
  title = {Solution of Dense Systems of Linear Equations in the Discrete-Dipole
	Approximation},
  journal = SJSC,
  year = {1996},
  volume = {17},
  pages = {78--89},
  number = {1}
}

@INPROCEEDINGS{dimacs95,
  author = {Gomathi Ramachandran and Tamar Schlick},
  title = {Beyond Optimization: Simulating the Dynamics of Supercoiled {DNA}
	by a Macroscopic Model},
  booktitle = {Global Minimization of Nonconvex Energy Functions: {M}olecular Conformation
	and Protein Folding},
  year = {1996},
  editor = {P. M. Pardalos and D. Shalloway and G. Xue},
  volume = {23},
  series = {{DIMACS} Series in Discrete Mathematics and Theoretical Computer
	Science},
  pages = {215--231},
  address = {Providence, Rhode Island},
  publisher = AMS
}

@ARTICLE{RAYM96,
  author = {I. Rayment},
  title = {Kinesin and myosin: molecular motors with similar engines},
  journal = STR,
  year = {1996},
  volume = {4},
  pages = {501--504}
}

@ARTICLE{Reic96,
  author = {S. Reich},
  title = {Enhancing Energy Conserving Methods},
  journal = {BIT Numer.\ Math.},
  year = {1996},
  volume = {36},
  pages = {122--134},
  number = {1},
  nack = {doe/nsf, nsf/arpa gcag, nih}
}

@ARTICLE{Reic96a,
  author = {S. Reich},
  title = {Symplectic Integration of Constrained {H}amiltonian Systems by Composition
	Methods},
  journal = SJNA,
  year = {1996},
  volume = {33},
  number = {2}
}

@ARTICLE{REIC96C,
  author = {S. Reich},
  title = {Torsion dynamics of molecular systems},
  journal = PRE,
  year = {1996},
  volume = {53},
  pages = {4176--4181},
  number = {4}
}

@ARTICLE{RESA96,
  author = {H. Resat and M. Mezei and J. A. McCammon},
  title = {Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {1426--1433}
}

@ARTICLE{RICC96,
  author = {M. Ricci and S. E. Bradforth and R. Jimenez and G. R. Fleming},
  title = {Internal Conversion and Energy Transfer Dynamics of Spheroidene in
	Soluti on and in the {LH}-1 and {LH}-2 Light-harvesting Complexes},
  journal = CPL,
  year = {1996},
  volume = {259},
  pages = {381--390}
}

@ARTICLE{RICH96,
  author = {H.-T. Richter and L. S. Brown and R. Needleman and J. K. Lanyi},
  title = {A Linkage of the {pKa's} of {A}sp-85 and {G}lu-204 Forms Part of
	the Reprotonation Switch of Bacteriorhodopsin},
  journal = BCH,
  year = {1996},
  note = {In press.}
}

@ARTICLE{RICO96,
  author = {S.~Le Ricousse and F.~Gouilleux and D.~Fortin and V.~Joulin and H.~Richard-Foys},
  title = {Glucocorticoid and progestin receptors are differently involved in
	the cooperation with a structural element of the mouse mammary tumor
	virus promoter},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {5072--5077}
}

@ARTICLE{RIIS96,
  author = {S. Riistama and A. Puustinen and A. {Garc{\'i}a-Horsman} and S. Iwata
	and H. Michel and M. Wikstr{\"o}m},
  title = {Channelling of dioxygen into the respiratory enzyme},
  journal = BBA,
  year = {1996},
  volume = {1275},
  pages = {1--4},
  number = {1-2}
}

@ARTICLE{ROCK96,
  author = {J.~K.~Rockhill and S.~R.~Wilson and R.~I.~Gumport},
  title = {2$'$-deoxy-7-(hydroxymethyl)-7-deazaadenosine -- {A} new analogue
	to model structural water in the major groove of the {DNA}.},
  journal = JACS,
  year = {1996},
  volume = {118},
  pages = {10065--10068},
  annote = {in press}
}

@ARTICLE{ROSE96A,
  author = {S.R. Rosenfeld and J.J. Correia and J. Xing and B. Rener and H.C.
	Cheung},
  title = {Structural studies of kinesin-nucleotide intermediates},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {30212--30221}
}

@ARTICLE{ROSE96,
  author = {S.R. Rosenfeld and B. Rener and J.J. Correia and M.S. Mayo and H.C.
	Cheung},
  title = {Equilibrium studies of kinesin-nucleotide intermediates},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {9473--9482}
}

@ARTICLE{ROUX96,
  author = {B. Roux and M. Nina and R. Pomes and J.C. Smith},
  title = {Thermodynamics Stability of water Molecules in the Bacteriorhodopsin
	Proton Channel - A Molecular Dynamics Free Energy Perturbation Study},
  journal = {Biophysical Journal},
  year = {1996},
  volume = {71},
  pages = {670--681}
}

@ARTICLE{SAAG96,
  author = {P.~T.~van der Saag},
  title = {Nuclear retinoid receptors: mediators of retinoid effects.},
  journal = EJCN,
  year = {1996},
  volume = {50},
  pages = {S24--S28},
  annote = {it's a review paper}
}

@ARTICLE{SABL96,
  author = {Elena P. Sablin and F. Jon Kull and Roger Cooke and Ronald D. Vale
	and Robert J. Fletterick},
  title = {Crystal structure of the motor domain of the kinesin-related motor
	ncd},
  journal = NAT,
  year = {1996},
  volume = {380},
  pages = {555--559}
}

@INPROCEEDINGS{SAND96,
  author = {Bilha Sandak and Ruth Nussinov and Haim J. Wolfson},
  title = {Docking of Conformationally Flexible Proteins},
  booktitle = {Proceedings of the 1996 Symposium on Combinatorial Pattern Matching,
	Lecture Notes in Computer Science, Vol. 1075},
  year = {1996},
  editor = {Dan Hirshberg and Gene Myers},
  publisher = {Springer Verlag}
}

@ARTICLE{SAND96a,
  author = {C. Sandmann and F. Cordes and W. Saenger},
  title = {Structure model of a complex between the {Factor for Inversion Stimulation
	(FIS)} and {DNA}: {Modeling} protein-{DNA} complexes with dyad symmetry
	and known protein structures},
  journal = PRO,
  year = {1996},
  volume = {25},
  pages = {486--500}
}

@ARTICLE{SANS96,
  author = {M. S. P. Sansom and I. D. Kerr and J. Breed and R. Sankararamakrishnan},
  title = {Water in Channel-Like Cavities: Structure and Dynamics},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {693--702}
}

@ARTICLE{SaPo96,
  author = {J.M. Sanz-Serna and A. Portillo},
  title = {Classical numerical integrators for wave-packet dynamics},
  journal = {J. Chem.\ Phys.},
  year = {1996},
  volume = {104},
  pages = {2349--2355},
  number = {6},
  nremark = {tech rept, Universidad de Valladolid, Valladolid, Spain}
}

@INCOLLECTION{SARK96,
  author = {Kakali Sarkar and Klaus Schulten},
  title = {Topology Representing Network in Robotics},
  booktitle = {Models of Neural Networks},
  publisher = {Springer--Verlag},
  year = {1996},
  editor = {J. Leo van Hemmen and Eytan Domany and Klaus Schulten},
  volume = {3},
  series = {Physics of Neural Networks},
  pages = {281--302},
  address = {New York},
  tbtechrep = {TB-93-15}
}

@ARTICLE{SAVA96,
  author = {H. Savage and M. Cyrklaff and G. Montoya and W. Kuhlbrandt and I.
	Sinning},
  title = {Two-dimensional Structure of Light Harvesting Complex II ({LHII})
	from the Purple Bacterium {R}hodovulum sulfidophilum and Comparison
	with {LHII} from {R}hodopseudomonas acidophila},
  journal = {Structure},
  year = {1996},
  volume = {4},
  pages = {243--252}
}

@ARTICLE{SAWI96,
  author = {D.A. Sawicki and R.S. Knox},
  title = {Universal relationship between optical emission and absorption of
	complex systems: An alternative approach},
  journal = {Phys.~Rev.~A},
  year = {1996},
  volume = {54},
  pages = {4837--4841}
}

@INCOLLECTION{SCHL96,
  author = {M. Schlenkrich and J. Brickmann and A. D. {MacKerell Jr.} and M.
	Karplus},
  title = {Empirical Potential Energy Function for Phospholipids: {C}riteria
	for Parameter Optimization and Applications},
  booktitle = {Biological Membranes: {A} Molecular Perspective from Computation
	and Experiment},
  publisher = {Birkhauser},
  year = {1996},
  editor = {K. M. Merz and B. Roux},
  pages = {31--81},
  address = {Boston},
  annote = {To cite CHARMM22 field for LIPIDS, cite this paper}
}

@ARTICLE{SCHO96,
  author = {G.D. Scholes},
  title = {Energy transfer and spectroscopic characterization of multichromophoric
	assemblies},
  journal = {J.~Phys.~Chem.},
  year = {1996},
  volume = {100},
  pages = {18731--18739}
}

@INPROCEEDINGS{SCHU96B,
  author = {Klaus Schulten and Michael Zeller},
  title = {Topology Representing Maps and Brain Function},
  booktitle = {Nova Acta Leopoldina NF},
  year = {1996},
  volume = {72},
  pages = {133--157},
  publisher = {Jahresversammlungsband},
  annote = {number=294}
}

@ARTICLE{SCHW96,
  author = {B. Schwartz and E. Bittner and O. Prezhdo and P. Rossky},
  title = {Quantum Decoherence and the Isotope Effect in Condensed Phase Nonadiabatic
	Molecular Dynamics Simulations},
  journal = JCP,
  year = {1996},
  volume = {104},
  pages = {5492--5955}
}

@ARTICLE{SELL96,
  author = {J.R. Sellers},
  title = {Kinesin and ncd, two structural cousins of myosin},
  journal = JMRCM,
  year = {1996},
  volume = {17},
  pages = {173--175}
}

@ARTICLE{Ball96b,
  author = {R.F. Service},
  title = {Folding Proteins Caught in the Act},
  journal = SCI,
  year = {1996},
  volume = {273},
  pages = {29},
  annote = {Research News article commenting on BALL96}
}

@INPROCEEDINGS{SHAR96,
  author = {R. Sharma and T. S. Huang and V. I. Pavlovic and K. Schulten and
	A. Dalke and J. Phillips and M. Zeller and W. Humphrey and Y. Zhao
	and Z. Lo and S. Chu},
  title = {Speech/gesture Interface to a Visual Computing Environment for Molecular
	Biologists},
  booktitle = {Proceedings of 13th ICPR 96},
  year = {1996},
  volume = {3},
  pages = {964--968}
}

@ARTICLE{SMAG96,
  author = {P. van der Smagt and F. Gr{\"o}n and K. Schulten},
  title = {Analysis and control of a rubbertuator arm},
  journal = BC,
  year = {1996},
  volume = {75},
  pages = {433--440}
}

@ARTICLE{SMIT96A,
  author = {C.A. Smith and I. Rayment},
  title = {X-ray structure of the magnesium ({II}).{ADP}.vanadate complex of
	the {{\em Dictyostelium discoideum}} myosin motor domain to 1.9\,{{\AA}}
	resolution},
  journal = BCH,
  year = {1996},
  volume = {35},
  pages = {5404--5417}
}

@ARTICLE{SMIT96,
  author = {Steven B. Smith and Yujia Cui and Carlos Bustamante},
  title = {Overstretching {B-DNA}: {The} Elastic Response of Individual Double-Stranded
	and Single-Stranded {DNA} Molecules},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {795--799}
}

@ARTICLE{SMIT96b,
  author = {W.L. Smith and D.L. DeWitt},
  title = {Prostaglandin Endoperoxide {H} Synthases-1 and -2},
  journal = AI,
  year = {1996},
  volume = {62},
  pages = {167--215}
}

@ARTICLE{SmFo96,
  author = {W. Smith and T.~R. Forester},
  title = {{DL\_POLY\_2.0}: A general-purpose parallel molecular dynamics simulation
	package},
  journal = JMG,
  year = {1996},
  volume = {14},
  number = {3},
  annote = {DL_POLY_2.0 is a general-purpose parallel molecular dynamics simulation
	package developed at Daresbury Laboratory under the auspices of the
	Council for the Central Laboratory of the Research Councils. Written
	to support academic research, it has a wide range of applications
	and is designed to run on a wide range of computers: from single
	processor workstations to parallel supercomputers. Its structure,
	functionality, performance, and availability are described.}
}

@ARTICLE{SMIT96c,
  author = {W.L. Smith and R.M. Garavito and D.L. DeWitt},
  title = {{Prostaglandin Endoperoxide H Synthases (Cyclooxygenases)-1 and -2}},
  journal = JBC,
  year = {1996},
  volume = {271},
  pages = {33157--33160},
  number = {52}
}

@ARTICLE{SOLO96,
  author = {Solomon, E. I. and Sundaram, U. M. and Machonkin, T. E.},
  title = {Multicopper Oxidases and Oxygenases},
  journal = CR,
  year = {1996},
  volume = {96},
  pages = {2563},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{SOMS96,
  author = {Oscar J. G. Somsen and Rienk {van Grondelle} and Herbert {van Amerongen}},
  title = {Spectral Broadening of Interacting Pigments: Polarized Absorption
	by Photosynthetic Proteins},
  journal = BJ,
  year = {1996},
  volume = {71},
  pages = {1934--1951}
}

@ARTICLE{STRI96,
  author = {T. R. Strick and J.-F. Allemand and D. Bensimon and A. Bensimon and
	V. Croquette},
  title = {The elasticity of a single supercoiled {DNA} molecule},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {1835--1837}
}

@ARTICLE{STRY96,
  author = {N.C.J. Strynadka and M. Eisenstein and E. Katchalski-Katzir and B.K.
	Shoichet and I.D. Kuntz and R. Abagyan and M. Totrov and J. Janin
	and J. Cherfils and F. Zimmerman and A. Olson and B. Duncan and M.
	Rao and R. Jackson and M. Sternberg and M.N.G. James},
  title = {Molecular Docking Programs Successfully Predict the Binding of a
	$\beta$-lactamase Inhibitory Protein to {TEM}-1 $\beta$-lactamase},
  journal = NATSB,
  year = {1996},
  volume = {3},
  pages = {233--239}
}

@BOOK{StHu96,
  title = {Dynamical Systems and Numerical Analysis},
  publisher = {Cambridge University Press},
  year = {1996},
  author = {A.M. Stuart and A.R. Humphries},
  address = {Cambridge, England}
}

@ARTICLE{StZB96,
  author = {S. J. Stuart and R. H. Zhou and B. J. Berne},
  title = {Molecular Dynamics with Multiple Time Scales---the Selection of Efficient
	Reference System Propagators},
  journal = {J. Chem.\ Phys.},
  year = {1996},
  volume = {105},
  pages = {1426---1436},
  number = {4},
  nremark = {particle-based rRESPA is not symplectic nor does it conserve momentum.
	Nor does there seem to be significant savings in not updating the
	positions of big masses every time step}
}

@ARTICLE{STUR96,
  author = {J. N. Sturgis and B. Robert},
  title = {The Role of Chromophore Coupling in Tuning the Spectral Properties
	of Peripheral Light-Harvesting Protein of Purple Bacteria},
  journal = {Photosynthesis Research},
  year = {1996},
  volume = {50},
  pages = {5--10}
}

@ARTICLE{SUNG96,
  author = {Shen-Shu Sung and Xiong-Wu Wu},
  title = {Molecular Dynamics Simulations of Synthetic Peptide Folding},
  journal = PRO,
  year = {1996},
  volume = {25},
  pages = {202--214}
}

@ARTICLE{THAI96,
  author = {S. Thaisrivongs and D.L. Romero and R.A. Tommasi and M.N. Janakiraman
	and J.W. Strohbach and S.R. Turner and C. Biles and R.R. Morge and
	P.D. Johnson and P.A. Aristoff and P.K. Tomich and J.C. Lynn and
	M.M. Horng and K.T. Chong and R.R. Hinshaw and W.J. Howe and B.C.
	Finzel and K.D. Watenpaugh},
  title = {Structure-Based Design of {HIV} Protease Inhibitors - 5,6-dihydro-4-hydroxy-2-pyrones
	as Effective, Nonpeptidic Inhibitors},
  journal = JMC,
  year = {1996},
  volume = {39},
  pages = {4630--4642}
}

@ARTICLE{TIEL96,
  author = {D.~P.~Tieleman and H.~J.~C.~Berendsen.},
  title = {Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine
	bilayer with different macroscopic boundary conditions and parameters},
  journal = JCP,
  year = {1996},
  volume = {105},
  pages = {4871--4880},
  annote = {uses DPPC and Gromos with different initial conditions: NpT, NVT,NgammaT}
}

@ARTICLE{TIMM96,
  author = {C.R. Timmel and P.J. Hore},
  title = {Oscillating magnetic field effects on the yields of radical pair
	reactions},
  journal = {Chem.~Phys.~Lett.},
  year = {1996},
  volume = {257},
  pages = {401}
}

@ARTICLE{Tino96,
  author = {I. Tinoco},
  title = {Nucleic Acid Structures, Energetics and Dynamics},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {13311--13322}
}

@ARTICLE{TIRI96,
  author = {M.M. Tirion},
  title = {Large Amplitude Elastic Motions in Proteins from a Single-Parameter
	Atomic Analysis},
  journal = PRL,
  year = {1996},
  volume = {77},
  pages = {1905--1908}
}

@ARTICLE{ToBo96,
  author = {A. Y. Toukmaji and J. A. Board},
  title = {{E}wald Summation Techniques in Perspective: A survey},
  journal = CPC,
  year = {1996},
  volume = {95},
  pages = {73--92},
  annote = {The simulation of large macromolecular systems has been and remains
	a challenging problem. There is a general presumption that simulations
	carried in periodic boundary conditions (PBC) are often the most
	appropriate to suppress boundary effects. To this end, Ewald summation
	has been employed to handle long ranged interactions in PBC. There
	has been a great deal of research targeted at improving the efficiency
	of Ewald summation, an (N2) algorithm in its traditional formulation,
	where N is the number of particles in the system. This paper reviews
	Ewald summation techniques by surveying conventional as well as state
	of the art efficient methods. Conventional methods, such as tabulation
	and approximation, are first re-examined along with an (N) method.
	Fourier-based approaches which have reduced the complexity to (N
	log (N)) are presented. Multipole expansion techniques, suggested
	as an alternative to Ewald sums, are reviewed and compared to Fourier
	methods. The computational efficiency of these new methods facilitates
	longer, larger and more realistic simulations.}
}

@ARTICLE{TSUK96,
  author = {T.\ Tsukihara and H.\ Aoyama and E.\ Yamashita and T.\ Tomizaki and
	H.\ Yamaguchi and K.\ Shinnzawha-Itoh and R.\ Nakashima and R.\ Yaono
	and S.\ Yoshikawa},
  title = {The Whole Structure of the 13-Subunit Oxidized Cytochrome c Oxidase
	at 2.8{{\AA}}},
  journal = SCI,
  year = {1996},
  volume = {272},
  pages = {1136--1144}
}

@ARTICLE{URA96,
  author = {K. Ura and K. Nightingale and A. Wolffe},
  title = {Differential association of {HMG1} and linker histones {B4} and {H1}
	with dinucleosomal {DNA} -- structural transitions and transcriptional
	repression},
  journal = EMBO,
  year = {1996},
  volume = {15},
  pages = {4959--4969},
  number = {18}
}

@ARTICLE{VALE96,
  author = {Ronald D. Vale},
  title = {Switches, Latches, and Amplifiers: Common Themes of {G}-Proteins
	and Molecular Motors},
  journal = JCB,
  year = {1996},
  volume = {135},
  pages = {291--302}
}

@ARTICLE{VKNJ96,
  author = {P. Vashishta and R. K. Kalia and A. Nakano and W. Jin},
  title = {Silica Under Very Large Positive and Negative Pressures - Molecular
	Dynamics Simulations on Parallel Computers},
  journal = { INTERNATIONAL-JOURNAL-OF-THERMOPHYSICS},
  year = {1996},
  volume = {17},
  pages = {169--178},
  number = {1},
  nabstract = {A highly efficient multiresolution algorithm has been developed to
	carry out large-scale molecular dynamics (MD) simulations for systems
	with long-range Coulomb and three-body covalent interactions. The
	algorithm combines the reduced cell and fast multipole methods and
	multiple time-step approach. Pressure-induced structural transformation,
	loss of intermediate range order, and dynamical correlations in SiO2
	glass are investigated with the molecular-dynamics method. At twice
	the normal density, the Si-O bond length increases, the Si-O coordination
	changes from 4 to 6, and the O-Si-O band-angle changes from 109 to
	90 degrees. This is a tetrahedral-to-octahedral transformation, which
	was reported by Meade, Hemley, and Mao. Results for phonon density
	of states also reveal significant changes at high pressures. The
	multiresolution MD approach has been used to investigate the structural
	properties and mechanical failure in microporous silica. Structural
	correlations are characterized by the fractal dimension, internal
	surface area, and pore surface-to-volume ratio. Critical behavior
	at fracture is analyzed in terms of pore percolation, and kinetic
	roughening of fractured surface is also investigated.}
}

@ARTICLE{VERK96,
  author = {A.S. Verkman and A.N. Van Hoek and T.H. Ma and A. Frigeri and W.R.
	Skach and A. Mitra and B.K. Tamarappoo and J. Farinas},
  title = {Water Transport Across Mammalian Cell Membranes},
  journal = AJOPCP,
  year = {1996},
  volume = {39},
  pages = {C12--C30}
}

@ARTICLE{VISS96,
  author = {H. M. Visser and O. J. G. Somsen and F. {van Mourik} and R. {van
	Grondelle}},
  title = {Excited State Energy Equillibration via Subpicosecond Energy Transfer
	within the Inhomogeneously Broadened Light-Harvesting Antenna of
	LH-1-Only {\em Rhodobacter sphaeroides} Mutants M2192 at Room Temperature
	and 4.2 K},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {18859--18867}
}

@ARTICLE{WBSS96,
  author = {M. Wagner and J. Bordner and F. Saied and S. Subramaniam},
  title = {Continuum Approaches to Membrane Electrostatics},
  journal = {Biophys.\ J.},
  year = {1996},
  volume = {70},
  pages = {A224}
}

@BOOK{WATT96,
  title = {Internet Programming With {P}ython},
  publisher = {M \& T Books},
  year = {1996},
  author = {Aaron Watters and Guido Van Rossum and James C. Ahlstrom}
}

@PHDTHESIS{WEBE96,
  author = {Wolfgang Weber},
  title = {Ein neues semiempirisces NDDO-Verfahren mit Orthogonalisierungskorrekturen:
	Entwicklung des Modells, Implementierung, Parametrisierung und Anwendungen},
  school = {Universit\"{a}t Z\"{u}rich, Philosphische Fakult\"{a}t II},
  year = {1996},
  address = {Z\"{u}rich, Switzerland}
}

@ARTICLE{WEIN96,
  author = {H. Weinstein and E. L. Mehler},
  title = {Structural change mechanisms in regulatory proteins},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {1792--1793}
}

@ARTICLE{WERN96,
  author = {M. H. Werner and A. M. Gronenborn and G. M. Clore},
  title = {Intercalation, {DNA} kinking, and the control of transcription},
  journal = SCI,
  year = {1996},
  volume = {271},
  pages = {778--784}
}

@ARTICLE{WIBE96,
  author = {Wiberg, K B and Rosenberg, R E},
  title = {Infrared Intensities: Cyclobutene. {A} Normal-Coordinate Analysis
	and Comparison with Cyclopropene},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {96},
  pages = {8282--8292}
}

@ARTICLE{WIDO96,
  author = {J.~Widom},
  title = {Short-range Order in Two Eukaryotic Genomes: Relation to Chromosome
	Structure},
  journal = JMB,
  year = {1996},
  volume = {259},
  pages = {579--588}
}

@ARTICLE{WILL96,
  author = {S. Williams and T. P. Cosgrove and R. Gilmanshin and K. S. Fang and
	R. H. Callendar and W. H. Woodruff and R. B. Dyer},
  title = {Fast events in protein folding,helix melting and formation in a small
	peptide},
  journal = {Biochemistry},
  year = {1996},
  volume = {36},
  pages = {691--698}
}

@ARTICLE{WILT96,
  author = {W. Wiltschko and R. Wiltschko},
  title = {Magnetic orientation in birds},
  journal = {J.~Exp.~Biol.},
  year = {1996},
  volume = {199},
  pages = {29--38}
}

@ARTICLE{WOOL96,
  author = {T.~B.~Woolf and B.~Roux},
  title = {Structure, energetics, and dynamics of lipid-protein interactions:
	a molecular dynamics study of the gramicidin {A} channel in a {DMPC}
	bilayer},
  journal = PSFG,
  year = {1996},
  volume = {24},
  pages = {92--114},
  annote = {uses DMPC membrane and charmm22 forcefield}
}

@ARTICLE{WU96,
  author = {H.-M. Wu and S. Savikhin and N. R. S. Reddy and R. Jankowiak and
	R. J. Cogdell and W. S. Struve and G. J. Small},
  title = {Femtosecond and Hole-Burning Studies of B800's Excitation Energy
	Relaxation Dynamics in the LH2 Antenna Complex of {\em Rhodopseudomonas
	acidophila} (Strain 10050)},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {12022--12033}
}

@ARTICLE{XU96,
  author = {Dong Xu and Charles Martin and Klaus Schulten},
  title = {Molecular Dynamics Study of Early Picosecond Events in the Bacteriorhodopsin
	Photocycle: Dielectric Response, Vibrational Cooling and the {J,
	K} Intermediates},
  journal = BJ,
  year = {1996},
  volume = {70},
  pages = {453--460},
  number = {1}
}

@ARTICLE{XU96A,
  author = {Dong Xu and James Christopher Phillips and Klaus Schulten},
  title = {Protein Response to External Electric Fields: Relaxation, Hysteresis
	and Echo},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {12108--12121},
  techrep = {TB-95-09}
}

@ARTICLE{XU96B,
  author = {Jing Xu and Mingyao Liu and Jason Liu and Isabella Caniggia and Martin
	Post},
  title = {Mechanical strain induces constitutive and regulated secretion of
	glycosaminoglycans and proteoglycans in fetal lung cells},
  journal = JOCS,
  year = {1996},
  volume = {109},
  pages = {1605--1613}
}

@ARTICLE{YANG96A,
  author = {L.~Q.~Yang and B.~M.~Pettitt},
  title = {{B} to {A} transition of {DNA} on the nanosecond time scale.},
  journal = JPC,
  year = {1996},
  volume = {100},
  pages = {2564--2566}
}

@ARTICLE{YANG96,
  author = {N.~N.~Yang and M.~Venugopalan and S.~Hardikar and A.~Glasebrook},
  title = {Identification of an estrogen response element activated by metabolites
	of 17$\Beta$--estradiol and raloxifene.},
  journal = SCI,
  year = {1996},
  volume = {273},
  pages = {1222--1225}
}

@ARTICLE{YGCP96,
  author = {Serhat Yesilyurt and Chahid K. Ghaddar and Manuel E. Cruz and Anthony
	T. Patera},
  title = {Bayesian-Validated Surrogates for Noisy Computer Simulations; Application
	to Random Media},
  journal = SJSC,
  year = {1996},
  volume = {17},
  pages = {973--992},
  number = {4}
}

@ARTICLE{YOUN96,
  author = {A.J. Young and H.A. Frank},
  title = {Energy transfer reactions involving carotenoids: quenching of chlorophyll
	fluorescence},
  journal = {Photochem.~Photobiol.~B},
  year = {1996},
  volume = {36},
  pages = {3--16}
}

@ARTICLE{ZAPP96,
  author = {V. Zappavigna and L. Falciola and M. H. Citterich and F. Mavillo
	and M. E. Bianchi},
  title = {{HMG1} interacts with {HOX} proteins and enhances their {DNA} binding
	and transcriptional activation},
  journal = EMBO,
  year = {1996},
  volume = {15},
  pages = {4981--4991},
  number = {18}
}

@INPROCEEDINGS{ZELL96,
  author = {Michael Zeller and Rajeev Sharma and Klaus Schulten},
  title = {Topology Representing Network for Sensor-Based Robot Motion Planning},
  booktitle = {Proceedings of the 1996 World Congress on Neural Networks},
  year = {1996},
  pages = {100--103},
  publisher = {{INNS} Press}
}

@INPROCEEDINGS{ZELL96A,
  author = {Michael Zeller and Rajeev Sharma and Klaus Schulten},
  title = {Vision-Based Motion Planning of a Pneumatic Robot Using a Topology
	Representing Neural Network},
  booktitle = {Proceedings of 1996 IEEE Int. Symposium on Intelligent Control},
  year = {1996},
  pages = {7--12}
}

@ARTICLE{ZHAN96,
  author = {Li Zhang and Jan Hermans},
  title = {Hydrophilicity of Cavities in Proteins},
  journal = PSFG,
  year = {1996},
  volume = {24},
  pages = {433--438},
  annote = {palcing of water with DOWSER}
}

@ARTICLE{ZHOU96,
  author = {Feng Zhou and Klaus Schulten},
  title = {Molecular Dynamics Study of the Activation of Phospholipase {$A_2$}
	on a Membrane Surface},
  journal = PRO,
  year = {1996},
  volume = {25},
  pages = {12--27},
  number = {1}
}

@ARTICLE{ZBLH96,
  author = {S. J. Zhou and D. M. Beazley and P. S. Lomdahl and B. L. Holian},
  title = {Dynamic Crack Processes via Molecular Dynamics},
  journal = {Physical Review Letters},
  year = {1996},
  volume = {76},
  pages = {2318--2321}
}

@TECHREPORT{Reic95c,
  author = {S. Reich},
  title = {Enhanced Long-Term Simulation of {H}amiltonian Systems Containing
	a Strong Non-convex Potential},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1995},
  number = {SC 95-32},
  month = DEC
}

@MISC{BaBr95,
  author = {Dov Bai and Achi Brandt},
  title = {Multiscale Methods in Molecular Dynamics},
  month = {October 12},
  year = {1995},
  note = {Overhead transparencies}
}

@MISC{Beck95,
  author = {O. Becker},
  title = {Reduced Variable Molecular Dynamics},
  month = {October 11},
  year = {1995},
  note = {Overhead transparencies}
}

@TECHREPORT{MoWu95b,
  author = {Jorge J. Mor{\'e} and Zhijun Wu},
  title = {Smoothing Techniques for Macromolecular Global Optimization},
  institution = {Argonne National Laboratory},
  year = {1995},
  number = {Preprint MCS-P542-0995},
  address = {9700 South Cass Avenue, Argonne, Illinois 60439},
  month = SEP
}

@BOOK{GoLa95,
  title = {Nonlinear Dynamics of Stiff Polymers},
  year = {1995},
  author = {Raymond E. Goldstein and Stephen A. Langer},
  volume = {75},
  number = {6},
  pages = {1094--1097},
  month = AUG,
  journal = {Phys.\ Rev.\ Lett.},
  nremark = {Jan hermans october 95}
}

@UNPUBLISHED{Zhan95,
  author = {Meiqing Zhang},
  title = {Stabilization of the {S}t\"ormer/{V}erlet Method},
  note = {Manuscript},
  month = JUL,
  year = {1995},
  annote = {July 28}
}

@INPROCEEDINGS{CRUZ95,
  author = {C. Cruz-Neira and P. Bash},
  title = {Integrating High-Performance Computing and Communications with Virtual
	Reality for Interactive Molecular Modeling: The VIBE system},
  booktitle = {The First Workshop on Simulation and Interaction in Virtual Environments,
	ACM SIVE'95},
  year = {1995},
  pages = {194--198},
  month = JUN
}

@TECHREPORT{Reic95b,
  author = {S. Reich},
  title = {A Free Energy Approach to the Torsion Dynamics of Macromolecules},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1995},
  number = {SC 95-17},
  month = JUN
}

@TECHREPORT{MoWu95a,
  author = {Jorge J. Mor{\'e} and Zhijun Wu},
  title = {Optimal Solutions to Distance Geometry Problems via Global Continuation},
  institution = {Argonne National Laboratory},
  year = {1995},
  number = {Preprint MCS-P520-0595},
  address = {9700 South Cass Avenue, Argonne, Illinois 60439},
  month = MAY
}

@INPROCEEDINGS{kale:mdl,
  author = {L. V. Kale and A. Gursoy},
  title = {Modularity, Reuse and Efficiency with Message-Driven Libraries},
  booktitle = {Proceedings of the $7^{th}$ SIAM Parallel Processing Conference},
  year = {1995},
  address = {San Fransisco, CA},
  month = FEB
}

@MASTERSTHESIS{Haye95,
  author = {Wayne Hayes},
  title = {Efficient Shadowing of High Dimensional Chaotic Systems with the
	Large Astrophysical {N}-body Problem as an Example},
  school = {Computer Science Dept., Univ. of Toronto},
  year = {1995},
  month = JAN,
  note = {M.Sc. Thesis}
}

@ARTICLE{BENA95,
  author = {Daniel ben-Avraham and Monique M. Tirion},
  title = {Dynamic and Elastic Properties of {F}-actin: A Normal-Modes Analysis},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {1231--1245}
}

@ARTICLE{ROIT95,
  author = {A. Roitberg, R.B. Gerber, R. Elber and M.A. Ratner},
  title = {Anharmonic wave functions of proteins: quantum self-consistent field
	calculations of {BPTI}},
  journal = SCI,
  year = {1995},
  volume = {268},
  pages = {1319}
}

@ARTICLE{Adam95,
  author = {R. L. P. ~Adams},
  title = {Eukaryotic {DNA} methyltransferases--structure and function.},
  journal = {BioEssays},
  year = {1995},
  volume = {17},
  pages = {139--145}
}

@ARTICLE{Agar95a,
  author = {Pankaj Agarwal},
  title = {The cell programming language},
  journal = {Artificial Life},
  year = {1995},
  volume = {2},
  pages = {3777},
  number = {1}
}

@ARTICLE{Agar95b,
  author = {Pankaj Agarwal},
  title = {Cellular Segregation and Engulfment Simulations Using the Cell Programming
	Language},
  journal = JTB,
  year = {1995},
  volume = {176},
  pages = {79},
  number = {1}
}

@ARTICLE{AjMu95,
  author = {Ajay and M.A. Murcko},
  title = {Computational Methods to Predict Binding Free Energy in Ligand-Receptor
	Complexes},
  journal = JMC,
  year = {1995},
  volume = {38},
  pages = {4953--4967}
}

@ARTICLE{ANDE95,
  author = {P.O. Andersson and S.M. Bachilo and R.-L. Chen and T. Gillbro},
  title = {Solvent and temperature effects on dual fluorescence in a series
	of carotenes. Energy gap dependence of the internal conversion rate},
  journal = {J.~Phys.~Chem.},
  year = {1995},
  volume = {99},
  pages = {16199--16209}
}

@ARTICLE{ANGE95,
  author = {A. Angerhofer and F Bornh{\"a}user and A. Gall and R.J. Cogdell},
  title = {Optical and optically detected magnetic resonance investigation on
	purple bacterial antenna complexes},
  journal = {Chem. Phys.},
  year = {1995},
  volume = {194},
  pages = {259--274}
}

@ARTICLE{ANOL95,
  author = {J.~H.~Anolik and C.~M.~Klinge and R.~Hilf and R.~Bambara},
  title = {Cooperative binding of Estrogen Receptor to {DNA} Depends on Spacing
	of Binding Sites, Flanking Sequence, and Ligand.},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {2511--2520}
}

@ARTICLE{AnMc95,
  author = {Antosiewicz, J. and Gilson, M.~K. and Lee, I.~H. and McCammon, J.~A.},
  title = {Acetylcholinesterase: Diffusional Encounter Rate Constants for Dumbbell
	Models of Ligand},
  journal = {Bioph.\ J.},
  year = {1995},
  volume = {68},
  pages = {62--68}
}

@ARTICLE{AuBe95,
  author = {P. Auffinger and D. L. Beveridge},
  title = {{A} simple test for evaluating the truncation effects in simulations
	of systems involving charged groups},
  journal = {Chem. Phys. Lett.},
  year = {1995},
  volume = {234},
  pages = {413}
}

@ARTICLE{BALA95,
  author = {S. P. Balashov and R. Govindjee and E. S. Imasheva and S. Misra and
	T. G. Ebrey and Y. Feng and R. K. Crouch and D. R. Menick},
  title = {The Two {p$K_a$}'s of Aspartate-85 and Control of Thermal Isomerization
	and Proton Release in the Arginine-82 to Lysine Mutant of Bacteriorhodopsin},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {8820--8834}
}

@ARTICLE{BALG95,
  author = {Ganesh Balgi and Deborah E. Leckband and Johannes M. Nitsche},
  title = {Transport Effects on the Kinetics of Protein-Surface Binding},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {2251--2260},
  annote = {june 1}
}

@ARTICLE{BaST95,
  author = {L. M. Barone and R. Simonazzi and A. Tenenbaum},
  title = {Molecular Dynamics on {APE}10},
  journal = CPC,
  year = {1995},
  volume = {90},
  pages = {44--58},
  number = {1}
}

@ARTICLE{BKLS95,
  author = {E. Barth and K. Kuczera and B. Leimkuhler and R.~D. Skeel},
  title = {Algorithms for Constrained Molecular Dynamics},
  journal = {J. Comput.\ Chem.},
  year = {1995},
  volume = {16},
  pages = {1192--1209},
  number = {10},
  nack = {NIH, DOE/NSF93}
}

@ARTICLE{BASS95,
  author = {D. Bassolino-Klimas and H. E. Alper and T. R. Stouch},
  title = {Mechanism of Solute Diffusion through Lipid Bilayer Membranes by
	Molecular Dynamics Simulation},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {4118--4129},
  annote = {june 1}
}

@ARTICLE{BAXE95,
  author = {A. D. Baxevanis and D. Landsman},
  title = {The {HMG-1} box protein family: classification and functional relationships},
  journal = NAR,
  year = {1995},
  volume = {23},
  pages = {1604--1613},
  number = {9}
}

@ARTICLE{BaGT95,
  author = {A. Bazzani and M. Giovannozzi and E. Todesco},
  title = {A program to compute {B}irkhoff normal forms of symplectic maps in
	R},
  journal = CPC,
  year = {1995},
  volume = {86},
  pages = {199--207},
  number = {1 and 2}
}

@ARTICLE{BEAT95,
  author = {M.~Beato and P.~Herrlich and G.~Sch{\"u}tz},
  title = {Steroid hormone receptors: many actors in search of a plot},
  journal = CEL,
  year = {1995},
  volume = {83},
  pages = {851--857}
}

@ARTICLE{BeSD95,
  author = {H.~J.~C. Berendsen and D. van der Spoel and R. van Drunen},
  title = {{GROMACS}: {A} message-passing parallel molecular dynamics implementation},
  journal = CPC,
  year = {1995},
  volume = {91},
  pages = {43--56}
}

@ARTICLE{BERG95,
  author = {B. van den Berg and M. Tessari and R. Boelens and R. Dijkman and
	G.H. de Haas and R. Kaptein and H.M. Verheij},
  title = {{NMR} structures of phospholipase {A$_2$} reveal conformational changes
	during interfacial activation},
  journal = {Nature Structural Biology},
  year = {1995},
  volume = {2},
  pages = {402--406}
}

@ARTICLE{BERG95a,
  author = {J. Bergeron and P. G. Frank and D. Scales and Q-H. Meng and G. Castro
	and Y. L. Marcel},
  title = {Apolipoprotein {A-I} Conformation in Reconstituted Discoidal Lipoproteins
	Varying in Phospholipid and Cholesterol Content},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {27429--27438}
}

@ARTICLE{BERL95,
  author = {E. Berliner and E.C. Young and K. Anderson and H.K. Mahtani and J.
	Gelles},
  title = {Failure of a single-headed kinesin to track parallel to microtubule
	protofilaments},
  journal = NAT,
  year = {1995},
  volume = {373},
  pages = {718--721}
}

@ARTICLE{Berm95,
  author = {C. Leonard Berman},
  title = {Grid-Multipole Calculations},
  journal = SJSC,
  year = {1995},
  volume = {16},
  pages = {1082--1091}
}

@INCOLLECTION{BISH95A,
  author = {Thomas C. Bishop and Helmut Heller and Klaus Schulten},
  title = {Molecular Dynamics on Parallel Computers: Applications for Theoretical
	Biophysics},
  booktitle = {Toward Teraflop Computing and New Grand Challenge Applications},
  publisher = {Nova Science Publishers, Inc., New York},
  year = {1995},
  editor = {Rajiv K. Kalia and Priya Vashishta},
  pages = {129--138}
}

@TECHREPORT{BoSc95,
  author = {F. A. Bornemann and Ch.\ Sch{\"u}tte},
  title = {A Mathematical Approach to Smoothed Molecular Dynamics: Correcting
	Potentials for Freezing Bond Angles},
  institution = {Konrad-Zuse-Zentrum f\"ur Informationstechnik Berlin},
  year = {1995},
  number = {SC 95-30}
}

@ARTICLE{BOUR95A,
  author = {W.~Bourguet and M.~Ruff and P.~Chambon and H.~Gronemeyer and D.~Moras},
  title = {Crystal structure of the ligand--binding domain of the human nuclear
	receptor {RXR}-${\alpha}$.},
  journal = NAT,
  year = {1995},
  volume = {375},
  pages = {377--382},
  annote = {2.7A resolution}
}

@ARTICLE{BOUR95,
  author = {P. E. Bourne and others},
  title = {The Macromolecular Crystallographic Information File {(mmCIF)}},
  journal = {Methods in Enzymology},
  year = {1995},
  note = {Submitted}
}

@ARTICLE{BrAM95,
  author = {M. Braxenthaler and F. Avbelj and J. Moult},
  title = {Structure and Energetics of Early Folding Units in Protein Folding:Analysis
	of a 1 ns Molecular Dynamics Trajectory of an Early Folding Unit
	in Water: The Helix I/Loop I-fragment of Barnase},
  journal = {J. Mol. Biol.},
  year = {1995},
  volume = {250},
  pages = {239--257}
}

@INPROCEEDINGS{BREN95,
  author = {S.E. Brenner and T.J.P. Hubbard},
  title = {A specification for defining and annotating regions of macromolecular
	structures},
  booktitle = {Proceedings of the Third International Conference on Intelligent
	Systems for Molecular Biology},
  year = {1995}
}

@ARTICLE{BROO95,
  author = {C. L. {Brooks III}},
  title = {Methodological Advances in Molecular Dynamics Simulations of Biological
	Systems},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {211--215},
  number = {2}
}

@ARTICLE{BroK85,
  author = { B.~Brooks and M.~Karplus},
  title = {Normal modes for specific modes of macromolecules: application to
	the hinge-bending mode of lysozyme},
  journal = PNAS,
  year = {1995},
  volume = {82},
  pages = {4995--4999}
}

@ARTICLE{BROW95,
  author = {L. S. Brown and J. Sasaki and H. Kandori and A. Maeda and R. Needleman
	and J. K. Lanyi},
  title = {{G}lutamic Acid 204 is the Terminal Proton Release Group at the Extracellular
	Surface of Bacteriorhodopsin},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {27122--27126}
}

@ARTICLE{Brug95,
  author = {F. Brug{\`e}},
  title = {A Mixed Geometric-Systolic Approach to Parallel Molecular Dynamics
	Simulations},
  journal = CPC,
  year = {1995},
  volume = {90},
  pages = {59--65},
  number = {1}
}

@ARTICLE{BRUK95,
  author = {I.~Brukner and R.~S{\'a}nchez},
  title = {Sequence-dependent bending propensity of {DNA} as revealed by {DNase}
	{I}: parameters for trinucleotides},
  journal = EMBO,
  year = {1995},
  volume = {14},
  pages = {1812--1818},
  number = {8}
}

@ARTICLE{BRYA95,
  author = {S. Bryant},
  title = {Statistics of Sequence-Structure Threading},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {236--244}
}

@ARTICLE{BBLS95,
  author = {J. Bryson and S. Betz and H. Lu and D. Suich and H. Zhou and K. O'Neil
	and W. DeGrado},
  title = {Protein Design: a Hierarchic Approach},
  journal = SCI,
  year = {1995},
  volume = {270},
  pages = {935--941}
}

@ARTICLE{Brus95,
  author = {R.~Br{\"u}sweiler},
  title = {Collective protein dynamics and nuclear spin relaxation},
  journal = JCP,
  year = {1995},
  volume = {102},
  pages = {3396-3403}
}

@ARTICLE{BURR95,
  author = {T.~P.~Burris and Z.~Nawaz and M.~J.~Tsai and B.~W.~O'Malley.},
  title = {A nuclear hormone receptor-associated protein that inhibits transactivation
	by the thyroid hormone and retinoic acid receptors},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {9525--9529}
}

@ARTICLE{CAFL95,
  author = {Amedeo Caflisch and Martin Karplus},
  title = {Acid and thermal denaturation of barnase investigaed by molecular
	dynamics and simulations},
  journal = JMB,
  year = {1995},
  volume = {252},
  pages = {672--708}
}

@ARTICLE{CANF94A,
  author = {J. M. Canfield and R. L. Belford and P. G. Debrunner and K. Schulten},
  title = {A Perturbation Treatment of Oscillating Magnetic Fields in the Radical
	Pair Mechanism Using the {Liouville} Equation},
  journal = CP,
  year = {1995},
  volume = {195},
  pages = {59--69},
  annote = {the same as CANF95A}
}

@ARTICLE{CANF95,
  author = {Jeff M. Canfield and R. Linn Belford and Peter G. Debrunner and Klaus
	Schulten},
  title = {A Perturbation Theory Treatment of Oscillating Magnetic Fields in
	the Radical Pair Mechanism},
  journal = CP,
  year = {1995},
  volume = {191},
  pages = {347--347}
}

@ARTICLE{CANF95A,
  author = {J. M. Canfield and R. L. Belford and P. G. Debrunner and K. Schulten},
  title = {A Perturbation Treatment of Oscillating Magnetic Fields in the Radical
	Pair Mechanism Using the {Liouville} Equation},
  journal = CP,
  year = {1995},
  volume = {195},
  pages = {59--69}
}

@ARTICLE{CHEN95,
  author = {H.~W.~Chen and M.~L.~Privalsky},
  title = {Cooperative formation of high--order oligomers by retinoid X receptors
	-- an unexpected mode of {DNA} recognition.},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {422--426}
}

@ARTICLE{CHES95,
  author = {B.~Cheskis and L.~P.~Freedman},
  title = {Modulation of nuclear receptor interactions by ligands: kinetic analysis
	using surface plasmon resonance.},
  journal = BCH,
  year = {1995},
  volume = {35},
  pages = {3309--3318}
}

@ARTICLE{CHIL95a,
  author = {Ashutosh Chilcotti and Thomas Boland and Buddy D. Ratner and Patrick
	S. Stayton},
  title = {The Relationship Between Ligand-Binding Thermodynamics and Protein-Ligand
	Interaction Forces Measured by Atomic Force Microscopy},
  journal = BJ,
  year = {1995},
  volume = {69},
  pages = {2125--2130},
  annote = {streptavidin mutants}
}

@ARTICLE{CHIL95,
  author = {Ashutosh Chilcotti and Patrick S. Stayton},
  title = {Molecular Origins of the Slow Streptavidin-Biotin Dissociation kinetics},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {10622--10628},
  annote = {streptavidin mutants}
}

@ARTICLE{CHIU95,
  author = {S.~W.~Chiu and M.~Clark and V.~Balaji and S.~Subramaniam and H.~L.~Scott
	and E.~Jakobsson},
  title = {Incorporation of surface tension into molecular dynamics simulations
	of an interface: a fluid phase lipid bilayer membrane},
  journal = BJ,
  year = {1995},
  volume = {69},
  pages = {1230--1245},
  annote = {uses DMPC membrane and Gromos}
}

@MISC{CHRIS95,
  author = {E.A.F. Christian and others},
  title = {{LEAP} (Version 1.0)},
  year = {1995},
  note = {University of California, San Francisco}
}

@ARTICLE{CHRI95,
  author = {J.~K.~Christman and S.~Nehls and L.~Polin and S.~C.~Brooks},
  title = {Relationship between Estrogen Structure and Conformational Changes
	in Estrogen Receptor/{DNA} Complexes.},
  journal = JSBMB,
  year = {1995},
  volume = {54},
  pages = {201--210},
  annote = {hormones do not interfere with the binding of ER to ERE but they
	have different effects on the conformation of the ER-ERE complex,i.e.,influence
	transcription}
}

@ARTICLE{CHUR95,
  author = {M. E. A. Churchill and D. N. M. Jones and T. Glaser and H. Hefner
	and M. A. Searles and A. A. Travers},
  title = {{HMG-D} is an architecture-specific protein that preferentially binds
	to {DNA} containing the dinucleotide {TG}},
  journal = EMBO,
  year = {1995},
  volume = {14},
  pages = {101--112},
  number = {7}
}

@ARTICLE{CLAR95,
  author = {J. B. Clarage and T. Romo and B. K. Andrews and B. M. Pettitt and
	G. N. Philips},
  title = {A sampling Problem in Molecular Dynamics Simulations of Macromolecules},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {3288--3292}
}

@ARTICLE{COHE95,
  author = {D. E. Cohen and M. R. Leonard},
  title = {Immobilized Artificial Membrane chromatography: A rapid and accurate
	{HPLC} method for predicting bile salt-membrane interactions},
  journal = {J.\ Lipid Research},
  year = {1995},
  volume = {36},
  pages = {2251--2260},
  number = {10}
}

@ARTICLE{COLE95,
  author = {B.~D. Coleman and I. Tobias and D. Swigon},
  title = {Theory of the influence of end conditions on self-contact in {DNA}
	loops},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {9101--9109},
  number = {20}
}

@ARTICLE{COLL95,
  author = {Jack R. Collins and Stanley K. Burt and John W. Erickson},
  title = {Flap opening in {HIV}-1 protease simulated by `activated' molecular
	dynamics},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {334--338}
}

@INCOLLECTION{CROF95,
  author = {Antony R. Crofts and Blanca Barquera and G. Bechmann and Marianna
	Guergova and R. Salcedo-Hernandez and B. Hacker and S. Hong and Robert
	B. Gennis},
  title = {Structure and Function in the bc1-complex of {\em {Rb}. sphaeroides}},
  booktitle = {Photosynthesis: from light to biosphere},
  publisher = {Kluwer Academic Publ., Dordrecht},
  year = {1995},
  editor = {P. Mathis}
}

@ARTICLE{DELA95,
  author = {J. K. Delaney and T. L. Brack and G. H. Atkinson and M. Ottolenghi
	and G. Steinberg and M. Sheves},
  title = {Primary Picosecond Molecular Events in the Photoreaction of the {BR5.12}
	Artificial Bacteriorhodopsin Pigment},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {2101--2105}
}

@ARTICLE{DCMP95,
  author = {Y. Deng and R. McCoy and R. Marr and R. Peierls and O. Yasar},
  title = {Molecular Dynamics on Distributed-Memory MIMD Computers with Load
	Balancing},
  journal = {Applied Math Letters},
  year = {1995},
  volume = {8},
  pages = {37--41},
  number = {3}
}

@TECHREPORT{DOED95,
  author = {E. J. Doedel and X. J. Wang},
  title = {{AUTO94}: {S}oftware for continuation and bifurcation problems in
	ordinary differential equations},
  institution = {Center for Research on Parallel Computing},
  year = {1995},
  number = {CRPC-95-2},
  address = {California Institute of Technology, Pacadena, CA 91125}
}

@ARTICLE{DoNe95,
  author = {S.A. Downie and S.A. Newman},
  title = {Different roles for fibronectin in the generation of fore and hind
	limb precartilage condensations},
  journal = {Dev. Biol.},
  year = {1995},
  volume = {172},
  pages = {519--530}
}

@ARTICLE{DrDr95,
  author = {Cristina I. Draghicescu and Mircea Draghicescu},
  title = {A Fast Algorithm for Vortex Blob Interactions},
  journal = {J. Comput.\ Physics},
  year = {1995},
  volume = {116},
  pages = {69--78},
  number = {1}
}

@ARTICLE{Dra+95,
  author = {D. Drasdo and R. Kree and J.S. Mc{C}askill},
  title = {{M}onte {C}arlo approach tissue-cell populations},
  journal = PRE,
  year = {1995},
  volume = {52},
  pages = {6635--6657}
}

@ARTICLE{DuPo95,
  author = {M.~J. Dudek and J.~W. Ponder},
  title = {Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins},
  journal = JCC,
  year = {1995},
  volume = {16},
  pages = {791--816},
  annote = {TINKER}
}

@ARTICLE{EDHO95,
  author = {O.~Edholm and O.~Berger and F.~Jahnig},
  title = {Structure and Fluctuations of Bacteriorhodopsin in the Purple Membrane:
	{A} molecular Dynamics Study},
  journal = JMB,
  year = {1995},
  volume = {250},
  pages = {95--111}
}

@ARTICLE{EISE95,
  author = {M.~Eisenstein and Z.~Shakked.},
  title = {Hydration patterns and intermolecular interactions in {A-DNA} crystal
	structures. Implications for {DNA} recognition},
  journal = JMB,
  year = {1995},
  volume = {248},
  pages = {662--678}
}

@TECHREPORT{Elli95,
  author = {William D. Elliot},
  title = {Multipole Algorithms for Molecular Dynamics Simulation on High Performance
	Computers},
  institution = {Dept.\ of Electrical Engineering, Duke Univ.},
  year = {1995},
  number = {95-003},
  note = {Also, Ph.D. thesis}
}

@ARTICLE{ENGE95,
  author = {M. Engels and K. Gerwert and D. Bashford},
  title = {Computational Studies of the Early Intermediates of the Bacteriorhodopsin
	Photocycle},
  journal = BPC,
  year = {1995},
  volume = {56},
  pages = {94--104}
}

@ARTICLE{ERIK95,
  author = {M.~A.~L.~Eriksson and T.~H{\"a}rd and L.~Nilsson},
  title = {Molecular Dynamics Simulations of the Glucocorticoid Receptor {DNA}-Binding
	Domain in Complex with {DNA} and Free in Solution},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {402--426},
  annote = {nilsson's simulations of the GR-DBD/DNA complex he used counterions,
	and cut-off, only measured bend of 10deg}
}

@ARTICLE{ERIK95A,
  author = {M.~A.~L.~Eriksson and L.~Nilsson},
  title = {Structure, thermodynamics and cooperativity of the glucocorticoid
	receptor {DNA}--binding domain in complex with different response
	elements. {Molecular} dynamics simulation and free energy perturbation
	study.},
  journal = JMB,
  year = {1995},
  volume = {253},
  pages = {453--472}
}

@ARTICLE{ERNS95,
  author = {J.A. Ernst and R.T. Clubb and H.-X. Zhou and A.M. Gronenborn and
	G.M. Clore},
  title = {Demonstration of Positionally Disordered Water Within a Protein Hydrophobic
	Cavity by {NMR}},
  journal = SCI,
  year = {1995},
  volume = {267},
  pages = {1813--1817}
}

@INCOLLECTION{ERWI95,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {A Critical Comparison of Models for Orientation and Ocular Dominance
	Columns in the Striate Cortex},
  booktitle = {Advances in Neural Information Processing Systems 7},
  publisher = {MIT Press},
  year = {1995},
  editor = {G. Tesauro and D. Touretzky and T. Leen},
  pages = {93--100},
  address = {Cambridge, Mass and London, England}
}

@ARTICLE{ERWI95A,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Models of Orientation and Ocular Dominance Columns in the Visual
	Cortex: A Critical Comparison},
  journal = NC,
  year = {1995},
  volume = {7},
  pages = {425--468},
  annote = {Technical report TB-94-08. Sumitted to "Neural Computation".},
  tbtechrep = {TB-94-08}
}

@ARTICLE{EsWa95,
  author = {P. {Espa{\~n}ol} and P. B. Warren},
  title = {Statistical Mechanics of Dissipative Particle Dynamics},
  journal = EPL,
  year = {1995},
  volume = {30},
  pages = {191--196},
  number = {4}
}

@ARTICLE{EPBD95,
  author = {U. Essmann and L. Perers and M. L. Berkowitz and T. Darden and H.
	Lee and L. G. Pedersen},
  title = {A smooth particle mesh {E}wald method},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {8577--8593},
  number = {19}
}

@ARTICLE{EVAN95,
  author = {E. Evans and K. Ritchie and R. Merkel},
  title = {Sensitive Force Technique to Probe Molecular Adhesion and Structural
	Linkages at Biological Interfaces},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {2580--2587},
  annote = {Cell adhesion. Has a review of various AFM experiments.}
}

@ARTICLE{FANN95,
  author = {YC. Fann and I. Ahmed and NJ. Blackburn and JS. Boswell and ML. Verkhovskaya
	and BM. Hoffman and M. Wikstr{\"o}m},
  title = {Structure of Cu-B In the Binuclear Heme-copper Center Of The Cytochrome
	Aa(3)-type Quinol Oxidase From Bacillus Subtilis - An {ENDOR} and
	{EXAFS} Study.},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {10245--10255},
  number = {32}
}

@ARTICLE{FELL95,
  author = {S.E. Feller and Y.H. Zhang and R.W. Pastor and B.R. Brooks},
  title = {Constant pressure molecular dynamics simulation - the {L}angevin
	piston method},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {4613--4621},
  number = {11}
}

@ARTICLE{FZPB95,
  author = {S.~E. Feller and Y.~Zhang and R.~W. Pastor and B.~R. Brooks},
  title = {Constant Pressure Molecular Dynamics Simulation: The {L}angevin Piston
	Method},
  journal = {J.\ Chem.\ Phys.},
  year = {1995},
  volume = {103},
  pages = {4613--4621},
  number = {11}
}

@ARTICLE{FERS95,
  author = {Alan Fersht},
  title = {Characterizing transition states in protein folding: an essencial
	step in the puzzle},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {79--84}
}

@ARTICLE{FETT95,
  author = {J. R. Fetter and J. Qian and J. Shapleigh and J. W. Thomas and A.
	{Garc{\'i}a-Horsman} and E. Schmidt and J. Hosler and G. T. Babcock
	and R. B. Gennis and S. {Ferguson-Miller}},
  title = {Possible proton relay pathways in cytochrome c oxidase},
  journal = {PNAS},
  year = {1995},
  volume = {92},
  pages = {1604--1608},
  annote = {copy}
}

@ARTICLE{FINN95,
  author = {B. E. Finn and J. Evenas and T. Drakenberg and J. P. Waltho and E.
	Thulin and S. Forsen},
  title = {Calcium-induced structural changes and domain autonomy in calmodulin},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {777--783}
}

@ARTICLE{FINZ95,
  author = {Laura Finzi and Jeff Gelles},
  title = {Measurement of lactose repressor-meditated loop formation and breakdown
	in single {DNA} molecules},
  journal = SCI,
  year = {1995},
  volume = {267},
  pages = {378--380}
}

@ARTICLE{FISH95,
  author = {A.J. Fisher and C.A. Smith and J.B. Thoden and R. Smith and K. Sutoh
	and H.M. Holden and I. Rayment},
  title = {X-ray structures of the myosin motor domain of {{\em Dictyostelium
	discoideum}} complexed with {MgADP.BeF$_x$} and {MgADP.AlF$_4^{-}$}},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {8960--8972}
}

@ARTICLE{FOTH95,
  author = {M. Fothergill and M.F. Goodman and J. Petruska and A. Warshel},
  title = {Structure-Energy Analysis of the Role of Metal Ions in Phosphodiester
	Bond Hydrolysis by {DNA} Polymerase {I}},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {11619--11627}
}

@ARTICLE{FRAG95,
  author = {G.~Fragoso and S.~John and M.~S.~Roberts and G.~L.~Hager},
  title = {Nucleosome positioning on the {MMTV} {LTR} results from the frequency-biased
	occupancy of multiple frames},
  journal = GAD,
  year = {1995},
  volume = {9},
  pages = {1933--1947}
}

@MANUAL{FRIS94,
  title = {Gaussian 94, Revision B.3},
  author = {M. J. Frisch and G. W. Trucks and H. B. Schlegel and P. M. W. Gill
	and B. G. Johnson and M. A. Robb and J. R. Cheeseman and T. Keith
	and G. A. Petersson and J. A. Montgomery and K. Raghavachari and
	M. A. Al-Laham and V. G. Zakrzewski and J. V. Ortiz and J. B. Foresman
	and C. Y. Peng and P. Y. Ayala and W. Chen and M. W. Wong and J.
	L. Andres and E. S. Replogle and R. Gomperts and R. L. Martin and
	D.~J. Fox and J. S. Binkley and D.~J. Defrees and J. Baker and J.
	P. Stewart and M. Head-Gordon and C. Gonzalez and J. A. Pople},
  organization = {Gaussian Inc.},
  address = {Pittsburgh, PA},
  year = {1995}
}

@ARTICLE{FRIS95,
  author = {D. Frishman and P. Argos},
  title = {Knowledge-based secondary structure assignment},
  journal = {Proteins: structure, function, and genetics},
  year = {1995},
  volume = {23},
  pages = {566--579}
}

@ARTICLE{GAGN95,
  author = {S.M. Gagne and S. Tsuda and M.X. Li and L.B. Smillie and B.D. Sykes},
  title = {Structures of the Troponin {C} Regulatory Domains in the Apo and
	Calcium-Saturated States},
  journal = {Nature Structural Biology},
  year = {1995},
  volume = {2},
  pages = {784--789}
}

@BOOK{GHJV95,
  title = {Design Patterns: Elements of Reusable Object-Oriented Software.},
  publisher = {Addison-Wesley},
  year = {1995},
  author = {E. Gamma and R. Helm and R. Johnson and J. Vlissides},
  address = {Reading, Massachusetts}
}

@ARTICLE{GARC95,
  author = {J. A. {Garc{\'i}a-Horsman} and A. Puustinen and R. B. Gennis and
	M. Wikstr{\"o}m},
  title = {Proton transfer in Cytochrome bo$_3$ Ubiquinol oxidase of {{\em E.
	coli}}: {S}econd-Site Mutations in {Subunit I} That Restore Proton
	Pumping in the Mutant {Asp135$\rightarrow$ASN}},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {4428--4433},
  annote = {copy}
}

@ARTICLE{GEOU95,
  author = {C. Geourjon and G. Deleage},
  title = {{SOPMA} - Significant Improvements in Protein Secondary Structure
	Prediction by Consensus Prediction from Multiple Alignments},
  journal = {Computer Applications in the Biosciences},
  year = {1995},
  volume = {11},
  pages = {681}
}

@ARTICLE{GERS95,
  author = {M. Gerstein and R. B. Altman},
  title = {Average Core Structures and Variability Measures for Protein Families:
	Application to the Immunoglobulins},
  journal = JMB,
  year = {1995},
  volume = {251},
  pages = {161--175}
}

@ARTICLE{GEWI95,
  author = {D.~T.~Gewirth and P.~Sigler},
  title = {The basis for half-site specificity explored through a non-cognate
	steroid receptor-{DNA} complex},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {386--394},
  annote = {shows that recognition of the non-consensus sequence is achieved
	by using water molecules - the structure used is messed up, includes
	TR,GR and ER peices, both the protein and the dna}
}

@ARTICLE{GILB95,
  author = {S.P. Gilbert and M.R. Webb and M. Brune and K.A. Johnson},
  title = {Pathway of processive {ATP} hydrolysis by kinesin},
  journal = NAT,
  year = {1995},
  volume = {373},
  pages = {671--676}
}

@ARTICLE{GILS95,
  author = {M. Gilson},
  title = {Theory of Electrostatics Interactions in Macromolecules},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {216--223}
}

@ARTICLE{GiMM95,
  author = {Michael K. Gilson and J. Andrew Mc{C}ammon and Jeffry D. Madura},
  title = {Molecular Dynamics Simulation with a Continuum Electrostatic Model
	of the Solvent},
  journal = JCC,
  year = {1995},
  volume = {16},
  pages = {1081--1095},
  number = {9}
}

@ARTICLE{GORI95,
  author = {A.~A.~Gorin and V.~B.~Zhurkin and W.~K.~Olson},
  title = {{B-DNA} twisting correlates with base-pair morphology},
  journal = JMB,
  year = {1995},
  volume = {247},
  pages = {34--48}
}

@ARTICLE{GOVI95,
  author = {R. Govindjee and M. Kono and S. P. Balashov and E. Imasheva and M.
	Sheves and T. G. Ebrey},
  title = {Effects of Substitution of Tyrosine 57 with Asparagine and Phenylalanine
	on the Properties of Bacteriorhodopsin},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {4828--4838}
}

@ARTICLE{GRIS95,
  author = {C.B. Grissom},
  title = {Magnetic field effects in biology: a survey of possible mechanisms
	with emphasis on radical-pair recombination},
  journal = {Chem.~Rev.},
  year = {1995},
  volume = {95},
  pages = {3--24}
}

@ARTICLE{GrPa95,
  author = {Dmitry G.\ Gromov and Juan J.\ de~Pablo},
  title = {Structure of Binary Polymer Blends: {M}ultiple Time Step Hybrid {M}onte
	{C}arlo Simulations and Self-Consistent Integral-Equation Theory},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {8247--8256},
  number = {18}
}

@ARTICLE{GRUB95,
  author = {Helmut Grubm{\"u}ller},
  title = {Predicting slow structural transitions in macromolecular systems:
	{C}onformational {F}looding},
  journal = PRE,
  year = {1995},
  volume = {52},
  pages = {2893--2906},
  number = {3}
}

@ARTICLE{WANG95,
  author = {Y. Guan and H. Zhang and R. and A. H.-J. Wang},
  title = {Electrostactic Potential Distribution of the Gene {V} Protein from
	{F}f Phage Facilitates Cooperative {DNA} Binding: A Model of the
	{GVP}-ss{DNA} Complex},
  journal = PS,
  year = {1995},
  volume = {4},
  pages = {187--197}
}

@INPROCEEDINGS{GuHT95,
  author = {W. F. van~Gunsteren and T. Huber and A. E. Torda},
  title = {Biomolecular modelling: Overview of types of methods to search and
	sample conformational space},
  booktitle = {AIP Conference Proceedings},
  year = {1995},
  volume = {330},
  pages = {253--268},
  publisher = {The first European conference on computational chemistry (E.C.C.C.1)},
  note = {Nancy, France}
}

@ARTICLE{HALG95a,
  author = {T. Halgren},
  title = {Potential Energy Functions},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {205--210}
}

@ARTICLE{HARD95,
  author = {C. H. Hardman and R. W. Broadhurst and A. R. C. Raine and K. D. Grasser
	and J. O. Thomas and E. D. Laue},
  title = {Structure of the {A}-domain of {HMG1} and its Interactions with {DNA}
	as Studied by Heteronuclear Three-~and Four-Dimensional {NMR} Spectroscopy},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {16596--16607},
  number = {51}
}

@ARTICLE{HaOk95,
  author = {D.~J. Hardy and D. I. Okunbor},
  title = {Qualitative Study of the Symplectic St\"ormer--Verlet Integrator},
  journal = {J. Chem.\ Phys.},
  year = {1995},
  volume = {102},
  pages = {8978--8982},
  number = {22},
  abstract = {Symplectic numerical integrators, such as the St\"ormer-Verlet method,
	are useful in preserving certain important properties that are not
	preserved by conventional numerical integrators. This paper analyzes
	the St\"ormer-Verlet method as applied to the simple harmonic model,
	which is an important model for molecular dynamics simulations. Restricting
	our attention to the one-dimensional case, both the exact solution
	and the St\"ormer-Verlet solution to this model are expressed as
	functions of the number of time steps taken, and then both of these
	functions are interpreted geometrically. The paper shows the existence
	of an upper bound on the error from the St\"ormer-Verlet method,
	and then an example is worked to demonstrate the closeness of this
	bound.},
  nack = {This work supported in part by the National Science Foundation Grant
	CCR-9408973.}
}

@ARTICLE{HARR95,
  author = {S.~C.~Harrison},
  title = {Principles of virus structure},
  journal = {Virology},
  year = {1995},
  address = {New York},
  publisher = {Raven}
}

@ARTICLE{Hend95,
  author = {Bruce Hendrickson},
  title = {The Molecule Problem: Exploiting Structure in Global Optimization},
  journal = {SIAM J. Optimization},
  year = {1995},
  volume = {5},
  number = {4}
}

@ARTICLE{HESS95,
  author = {S. Hess and M. Chachisvilis and K. Timpmann and M.R. Jones and G.J.S.
	Fowler and C.N. Hunter and V. Sundstrom},
  title = {Temporally and Spectrally Resolved Subpicosecond Energy Transfer
	Within the Peripheral Antenna Complex ({LH2}) and from {LH}2 to the
	Core Antenna Complex in Photosynthetic Purple Bacteria},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {12333--12337}
}

@ARTICLE{HeSt95,
  author = {B. Hesselbo and R. B. Stinchcombe},
  title = {{M}onte {C}arlo Simulation and Global Optimization Without Parameters},
  journal = prl,
  year = {1995},
  volume = {74},
  pages = {2151--2155},
  annote = {$1/k$ sampling reference, in Schu99}
}

@ARTICLE{HIRO95,
  author = {Keiko Hirose and Andrew Lockhart and Robert A. Cross and Linda A.
	Amos},
  title = {Nucleotide-dependent angular change in kinesin motor domain bound
	to tubulin},
  journal = NAT,
  year = {1995},
  volume = {376},
  pages = {277--279}
}

@ARTICLE{HIRS95,
  author = {J. D. Hirst and C. L. Brooks},
  title = {Molecular Dynamics Simulations of isolated Helices of Myoglobin},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {7614--7621},
  number = {23}
}

@ARTICLE{HOEN95,
  author = {A. Hoenger and E. P. Sablin and R. D. Vale and R. J. Fletterick and
	R. A. Milligan},
  title = {Three-dimensional structure of a tubulin-motor-protein complex},
  journal = NAT,
  year = {1995},
  volume = {376},
  pages = {271--274}
}

@ARTICLE{HOLV95,
  author = {P. Holvoet and Z. Zhao and B. Vanloo and R. Vos and E. Deridder and
	A. Dhoest and J. Taveirne and E. Brouwers and E. Demarsin and Y.
	Engelborghs and M. Rosseneu and D. Collen and R. Brasseur},
  title = {Phospholipid Binding and Lecithin-Cholesterol Acyltransferase Activation
	Properties of Apolipoprotein {A-I} Mutants},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {13334--13342}
}

@ARTICLE{HONG95,
  author = {Felix T. Hong},
  title = {Magnetic field effects on biomolecules, cells, and living organisms},
  journal = {BioSystems},
  year = {1995},
  volume = {36},
  pages = {187--229}
}

@ARTICLE{HONI95,
  author = {B. Honig and A. Nicholls},
  title = {Classical Electrostatics in Biology and Chemistry},
  journal = SCI,
  year = {1995},
  volume = {268},
  pages = {1144--1149}
}

@ARTICLE{HOWA95,
  author = {Jonathon Howard},
  title = {The Mechanics of Force Generation by Kinesin},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {245s-255s}
}

@ARTICLE{HU95,
  author = {Xiche Hu and Dong Xu and Kenneth Hamer and Klaus Schulten and J{\"u}rgen
	Koepke and Hartmut Michel},
  title = {Predicting the Structure of the Light-Harvesting Complex {II} of
	{{\em Rhodospirillum molischianum}}},
  journal = PS,
  year = {1995},
  volume = {4},
  pages = {1670--1682}
}

@ARTICLE{HUMP95,
  author = {William Humphrey and Dong Xu and Mordechai Sheves and Klaus Schulten},
  title = {Molecular Dynamics Study of the Early Intermediates in the Bacteriorhodopsin
	Photocycle},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {14549--14560},
  annote = {submitted on Feb. 8th, 95; [Beckman Institute Technical Report TB-95-05]}
}

@ARTICLE{HUNE95A,
  author = {P. H. Hunenberger and A. E. Mark and W. van~Gunsteren},
  title = {Computational Approaches to Study Protein Unfolding: Hen Egg White
	Lysozyme as a Case Study},
  journal = PRO,
  year = {1995},
  volume = {21},
  pages = {196--213}
}

@ARTICLE{HUNE95,
  author = {P.~H.~Hunenberger and A.~E.~Mark and W.~F.~van Gunsteren},
  title = {Fluctuation and cross-correlation analysis of protein motions observed
	in nanosecond molecular dynamics simulations.},
  journal = JMB,
  year = {1995},
  volume = {252},
  pages = {175--194}
}

@ARTICLE{HDSH95,
  author = {Y.-S. Hwang and R. Das and J.~H. Saltz and M. Hodo{{\v s}\v c}ek
	and B.~R. Brooks},
  title = {Parallelizing Molecular Dynamics Programs for Distributed-Memory
	Machines},
  journal = {IEEE Computational Science \& Engineering},
  year = {1995},
  volume = {2},
  pages = {18--29},
  number = {2}
}

@ARTICLE{IiCS95,
  author = {T. Iitaka and N. Carjan and D. Strottman},
  title = {Stability of the Symmetric Multistep Methods for the Time-Dependent
	Schr\"odinger Equation},
  journal = {Comput.\ Phys.\ Commun.},
  year = {1995},
  volume = {90},
  pages = {251--259},
  number = {1 and 2}
}

@ARTICLE{ISAM95,
  author = {H. Isambert and P. Venier and A. C. Maggs and A. Fattoum and R. Kassab
	and D. Pantaloni and M. F. Carlier},
  title = {Flexibility of actin filaments derived from thermal fluctuations},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {11437--11444}
}

@ARTICLE{IWAT95,
  author = {S. Iwata and C. Ostermeier and B. Ludwig and H. Michel},
  title = {Structure at 2.8 {{\AA}} Resolution of Cytochrome {\it C} Oxidase
	From {{\it Paracoccus denitrificans}}},
  journal = NAT,
  year = {1995},
  volume = {376},
  pages = {660--669}
}

@ARTICLE{JAIN95,
  author = {M. K. Jain and M.H. Gelb and J. Rogers and O.G. Berg},
  title = {Kinetic basis for interfacial catalysis by phospholipase {A}$_2$},
  journal = {Methods in enzymology},
  year = {1995},
  volume = {249},
  pages = {567--614}
}

@ARTICLE{JaMe95,
  author = {D. Jane\v{z}i\v{c} and F. Merzel},
  title = {An Efficient Symplectic Integration Algorithm for Molecular Dynamics
	Simulations},
  journal = {J. Chem.\ Inf.\ Comput.\ Sci.},
  year = {1995},
  volume = {35},
  pages = {321--326}
}

@ARTICLE{JEFF95,
  author = {Philip D. Jeffrey and J{\"u}rgen Bajorath and ChiehYing Y. Chang
	and Dale Yelton and Ingegerd Hellstr{\"o}m and Karl Erik Hellstr{\"o}m
	and Steven Sheriff},
  title = {The {X}-Ray Structure of an Anti-Tumor Antibody in Complex with Antigen},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {466--471},
  number = {6}
}

@ARTICLE{JI95,
  author = {Y. Ji and A. Jonas},
  title = {Properties of an {N}-Terminal Proteolytic Fragment of Apolipoprotein
	{A-I} in Solution and in Reconstituted High Density Lipoproteins},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {11290--11297}
}

@ARTICLE{JoWG95,
  author = {Jones, G and Willet, P and Glen, RC},
  title = {Molecular recognition of receptor sites using a genetic algorithm
	with a description of desolvation},
  journal = JMB,
  year = {1995},
  volume = {245},
  pages = {43--53}
}

@ARTICLE{JUNG95,
  author = {P. Jungwirth and R.B. Gerber},
  title = {Quantum dynamics of large polyatomic systems using a classically
	based separable potential method},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {102},
  pages = {6046},
  number = {15}
}

@ARTICLE{KAND95,
  author = {H.~Kandori and Y.~Yamazaki and J.~Sasaki and R.~Needleman and J.~K.~Lanyi
	and A.~Maeda},
  title = {Water-Mediated Proton Transfer in Proteins: An {FTIR} Study of Bacteriorhodopsin},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {2118--2119}
}

@ARTICLE{KANZ95,
  author = {M. Kanzaki and A Iwasawa},
  title = {A Sensitive, Non-Isotopic Immunoassay for Progesterone Using the
	Avidin-Biotin System},
  journal = BR,
  year = {1995},
  volume = {16},
  pages = {381--386},
  number = {6},
  annote = {june 1}
}

@ARTICLE{KARP95,
  author = {Martin Karplus and Andrej Sali},
  title = {Theoretical studies of protein folding and unfolding},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {58--73}
}

@ARTICLE{KARR95,
  author = {S. Karrasch and P.A. Bullough and R. Ghosh},
  title = {{8.5\,\AA\ } projection map of the light-harvesting complex {I} from
	{{\em {R}hodospirillum rubrum}} reveals a ring composed of 16 subunits},
  journal = {EMBO J.},
  year = {1995},
  volume = {14},
  pages = {631}
}

@ARTICLE{KELL95,
  author = {W.~Keller and P.~K{\"o}nig and T.~J.~Richmond},
  title = {Crystal structure of a {bZIP/DNA} complex at 2.2 {\AA}: {D}eterminants
	of {DNA} specific recognition.},
  journal = JMB,
  year = {1995},
  volume = {254},
  pages = {657--667},
  number = {4}
}

@ARTICLE{KODA95,
  author = {T.~Kodadek},
  title = {From carpet bombing to cruise missiles: the 'second-order' mechanism
	used by transcription factors to ensure specific {DNA} binding \em
	in vivo.},
  journal = CHB,
  year = {1995},
  volume = {2},
  pages = {267--279},
  annote = {review paper}
}

@ARTICLE{KoSc95,
  author = {Jaroslaw Kostrowicki and Harold A. Scheraga},
  title = {Simple Global Minimization Algorithm for One-Variable Rational Functions},
  journal = {J. Global Optimization},
  year = {1995},
  volume = {6},
  pages = {293--311},
  number = {3}
}

@ARTICLE{KoDS95,
  author = {R. E. Kozack and M.~J. D'Mello and S. Subramaniam},
  title = {Computer Modeling of Electrostatic Steering and Orientational Effects
	in Antibody--Antigen Association},
  journal = {Biophys.\ J.},
  year = {1995},
  volume = {68},
  pages = {807--814}
}

@ARTICLE{KUBO95,
  author = {H. Kuboniwa and N. Tjandra and S. Grzesiek and H. Ren and C. B. Klee
	and A. Bax},
  title = {Solution structure of calcium-free calmodulin.},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {768--776}
}

@ARTICLE{KURR94,
  author = {Christian Kurrer and Klaus Schulten},
  title = {Noise-Induced Neuronal Oscillations},
  journal = PRE,
  year = {1995},
  volume = {51},
  pages = {6213--6218},
  number = {6},
  annote = {[Beckman Institute Technical Report TB-93-16]; this paper is the
	same as KURR95},
  tbtechrep = {TB-93-16}
}

@ARTICLE{KURR95,
  author = {Christian Kurrer and Klaus Schulten},
  title = {Noise-Induced Neuronal Oscillations},
  journal = PRE,
  year = {1995},
  volume = {51},
  pages = {6213--6218},
  number = {6},
  annote = {[Beckman Institute Technical Report TB-93-16]},
  tbtechrep = {TB-93-16}
}

@ARTICLE{LABE95,
  author = {S. Labeit and B. Kolmerer},
  title = {Titins, giant proteins in charge of muscle ultrastructure and elasticity},
  journal = SCI,
  year = {1995},
  volume = {270},
  pages = {293--296}
}

@INPROCEEDINGS{LANC95,
  author = {C.R.D. Lancaster and U. Ermler and H. Michel},
  title = {The Structure of Photosynthetic Reaction Centers from Purple Bacteria
	as Revealed by X-Ray Crystallography},
  booktitle = {Anoxygenic Photosynthetic Bacteria},
  year = {1995},
  editor = {R.E. Blankenship and M.T. Madigan and C.E. Bauer},
  pages = {503--526},
  address = {Dordrecht},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{LANY95,
  author = {J. Lanyi},
  title = {Bacteriorhodopsin as a Model for Proton Pumps.},
  journal = NAT,
  year = {1995},
  volume = {375},
  pages = {461--463}
}

@ARTICLE{LAWL95,
  author = {Lawless, M K and Wickham, S D and Mathies, R A},
  title = {Resonance {Raman} View of Pericyclic Photochemical Ring-Opening Reactions:
	Beyond the Woodward-Hoffman Rules},
  journal = {Acc. Chem. Res.},
  year = {1995},
  volume = {28},
  pages = {493--502}
}

@ARTICLE{LEE95,
  author = {J.~W.~Lee and F.~Ryan and J.~C.~Swaffield and S.~A.~Johnston and
	D.~D.~Moore.},
  title = {Interaction of thyroid--hormone receptor with a conserved transcriptional
	mediator},
  journal = NAT,
  year = {1995},
  volume = {374},
  pages = {91--94}
}

@ARTICLE{LERA95,
  author = {Angel R. de Lera and Beatriz Iglesias and Jes{\'u}s Rodr\'{i}guez
	and Rosana Alvarez and Susana L{\'o}pez and Xavier Villanueva and
	Esteve Padr{\'o}s},
  title = {Experimental and Theoretical Analysis of the Steric Tolerance of
	the Binding Site of Bacterioopsin with the Use of Side-Chain Methyl-Shifted
	Retinal Analogs},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {8220--8231}
}

@ARTICLE{LEVI95,
  author = {M. Levitt and M. Hirshberg and R. Sharon and V. Daggett},
  title = {Potential Energy Function and Parameters for Simulations of the Molecular
	Dynamics of Proteins and Nucleic Acids in Solution},
  journal = CPC,
  year = {1995},
  volume = {91},
  pages = {215--231}
}

@ARTICLE{LHSD95,
  author = {M. Levitt and M. Hirshberg and R. Sharon and V. Daggett},
  title = {Potential Energy Function and Parameters for Simulations of the Molecular
	Dynamics of Proteins and Nucleic Acids in Solution},
  journal = CPC,
  year = {1995},
  volume = {91},
  pages = {215--231}
}

@ARTICLE{LIM95,
  author = {K. Lim and J. N. Herron},
  title = {Molecular Dynamics of the Anti-Fluorescein 4-4-20 Antigen-Binding
	Fragment. 1. Computer Simulations},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {6962--6974}
}

@ARTICLE{LIU95,
  author = {H. Liu and S. Ong and L. Glunz and C. Pidgeon},
  title = {Predicting Drug - Membrane Interactions by {HPLC}: Structural Requirements
	of Chromotographic Surfaces},
  journal = {Analytical Chemistry},
  year = {1995},
  volume = {67},
  pages = {3550--3557}
}

@ARTICLE{LOCK95,
  author = {A. Lockhart and R.A. Cross and D.F.A. McKillop},
  title = {{ADP} release is the rate-limiting step of the {MT} activated {ATP}ase
	of non-claret disjunctional and kinesin},
  journal = FEBS,
  year = {1995},
  volume = {368},
  pages = {531--535}
}

@ARTICLE{LOGU95C,
  author = {Ilya Logunov and William Humphrey and Klaus Schulten and Mordechai
	Sheves},
  title = {Molecular Dynamics Study of the 13-{\it cis} Form ({bR}$_{548}$)
	of Bacteriorhodopsin and Its Photocycle},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {1270--1282},
  tbtechrep = {TB-94-20}
}

@INPROCEEDINGS{LOGU95,
  author = {Ilya Logunov and Klaus Schulten},
  title = {Quantum Chemistry of {\it in situ} Retinal: Study of the Spectral
	Properties and Dark Adaptation of Bacteriorhodopsin},
  booktitle = {Proceedings of the Ecole de Physique des Houches},
  year = {1995},
  editor = {D. Bicout and M. J. Field},
  pages = {235--256},
  address = {Paris},
  publisher = {Les Editions de Physique, Springer}
}

@ARTICLE{LOGU95B,
  author = {Ilya Logunov and Klaus Schulten},
  title = {Quantum Chemistry -- Molecular Dynamics Study of the Optical Spectrum
	of Bacteriorhodopsin},
  journal = JPC,
  year = {1995},
  note = {Under revision. [Beckman Institute Technical Report TB-95-24].},
  techrep = {TB-95-24}
}

@ARTICLE{LOVE95,
  author = {J. J. Love and X. Li and D. A. Case and K. Giese and R. Grosschedl
	and P. E. Wright},
  title = {Structural basis for {DNA} bending by the architectural transcription
	factor {LEF-1}},
  journal = NAT,
  year = {1995},
  volume = {376},
  pages = {791--795}
}

@ARTICLE{LUDL95,
  author = {C. F. C. Ludlam and S. Sonar and C. P. Lee and M. Coleman and J.
	Herzfeld and U. L. Rajbhandary and K. J. Rothschild},
  title = {SITE-DIRECTED ISOTOPE LABELING AND {ATR-FTIR} DIFFERENCE SPECTROSCOPY
	OF BACTERIORHODOPSIN - THE PEPTIDE CARBONYL GROUP OF TYR 185 IS STRUCTURALLY
	ACTIVE DURING THE {bR} $\rightarrow$ {N} TRANSITION},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {2--6}
}

@ARTICLE{LUEC95,
  author = {Hartmut L{\"u}cke and Bryna T. Chang and William S. Mailliard and
	David D Schlaepfer and Harry T Haigler},
  title = {Crystal structure of annexin {XII} hexamer and implications for bilayer
	insertion},
  journal = NAT,
  year = {1995},
  volume = {378},
  pages = {512--515},
  number = {6556}
}

@ARTICLE{MA95,
  author = {Y.-Z. Ma and E.W. Taylor},
  title = {Kinetic mechanism of kinesin motor domain},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {13233--13241}
}

@ARTICLE{MA95A,
  author = {Y.-Z. Ma and E.W. Taylor},
  title = {Mechanism of Microtubule Kinesin {ATP}ase},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {13242--13251}
}

@ARTICLE{MACK95,
  author = {A. D. {MacKerell Jr.} and J. {Wiorkiewicz-Kuczera} and M. Karplus},
  title = {An all-atom empirical energy function for the simulation of nucleic
	acids},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {11946--11975},
  number = {48},
  annote = {To cite CHARMM22 field for NUCLEIC ACIDS, cite this paper}
}

@ARTICLE{MALA95,
  author = {F. Malatesta and G. Antonioni and P. Sarti and M. Brunori},
  title = {Structure and function of a molecular machine: cytochrome c oxidase},
  journal = {Biophysical Chemistry},
  year = {1995},
  volume = {54},
  pages = {1--33},
  annote = {review}
}

@ARTICLE{MaSc95,
  author = {Margaret Mandziuk and Tamar Schlick},
  title = {Resonance in the Dynamics of Chemical Systems Simulated by the Implicit
	Midpoint Scheme},
  journal = {Chem.\ Phys.\ Letters},
  year = {1995},
  volume = {237},
  pages = {525--535}
}

@ARTICLE{MANG95,
  author = {D.~J.~Mangelsdorf and C.~Thummel and M.~Beato and P.~Herrlich and
	G.~Schutz and K.~Umesono and B.~Blumberg and P.~Kastner and M.~Mark
	and P.~Chambon and R.~M.~Evans},
  title = {The nuclear receptor superfamily: the second decade.},
  journal = {Cell},
  year = {1995},
  volume = {83},
  pages = {835--839},
  annote = {review paper with hormone structures}
}

@ARTICLE{MARK95,
  author = {J. Marko and E. Siggia},
  title = {Stretching {D}{N}{A}},
  journal = MA,
  year = {1995},
  volume = {28},
  pages = {8759--8770}
}

@ARTICLE{MART95,
  author = {G. J. Martyna and M. E. Tuckerman},
  title = {Symplectic Reversible Integrators: Predictor-Corrector Methods},
  journal = JCP,
  year = {1995},
  volume = {102},
  pages = {8071--8077},
  number = {20}
}

@ARTICLE{MaTu95,
  author = {Glenn J. Martyna and Mark E. Tuckerman},
  title = {Symplectic Reversible Integrators: Predictor-Corrector Methods},
  journal = JCP,
  year = {1995},
  volume = {102},
  pages = {8071--8077},
  number = {20}
}

@ARTICLE{MART95A,
  author = {G. J. Martyna and M. E. Tuckerman and D.~J. Tobias and M. L. Klein},
  title = {Explicit Reversible Integrators for Extended System Dynamics},
  year = {1995},
  note = {sent to Molecular Physics, May, 1995}
}

@ARTICLE{MCDE95,
  author = {G. McDermott and S.M. Prince and A.A. Freer and A.M. Hawthornthwaite-Lawless
	and M.Z. Papiz and R.J. Cogdell and N.W. Isaacs},
  title = {Crystal structure of an integral membrane light-harvesting complex
	from photosynthetic bacteria},
  journal = NAT,
  year = {1995},
  volume = {374},
  pages = {517--521}
}

@ARTICLE{McSc95,
  author = {R.I. McLachlan and J.C. Scovel},
  title = {Equivariant Constrained Symplectic Integration},
  journal = {Nonlinear Sci.},
  year = {1995},
  volume = {5},
  pages = {233--256}
}

@ARTICLE{McLa95,
  author = {Robert I. McLaughlin},
  title = {Composition Methods in the Presence of Small Parameters},
  journal = {BIT Numer.\ Math.},
  year = {1995},
  volume = {35},
  pages = {258--268},
  number = {2}
}

@ARTICLE{MeOt95,
  author = {M. Melchior and H.C. {{\"O}ttinger}},
  title = {Variance Reduced Simulations of Stochastic Differential Equations},
  journal = {J.Chem.\ Phys.},
  year = {1995},
  volume = {103},
  pages = {9506--9509},
  number = {21},
  annote = {Use importance samplings for brownian dynamics. How to do a change
	of unerlying probability space, i.e. use a non-uniform sampling probability
	and relate the average in the new prob. space to the old one. Also
	mention the optimal sampling probability. Application to bead-spring
	<QQ> with HI.}
}

@ARTICLE{MICK95,
  author = {B. Mickey and J. Howard},
  title = {Rigidity of Microtubules is Increased by Stabilizing Agents},
  journal = JCB,
  year = {1995},
  volume = {130},
  pages = {909--917}
}

@ARTICLE{MITR95,
  author = {A.K. Mitra and A.N. Van Hoek and M.C. Wiener and A.S. Verkman and
	M. Yeager},
  title = {The {CHIP28} Water Channel Visualized in Ice by Electron Crystallography},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {726}
}

@ARTICLE{MIXO95,
  author = {M. B. Mixon and E. Lee and D. E. Coleman and A. M. Berghuis and A.
	G. Gilman and S. R. Sprang},
  title = {Tertiary and quaternary structural changes in {G$_{i\alpha1}$} induced
	by {GTP} hydrolysis},
  journal = SCI,
  year = {1995},
  volume = {270},
  pages = {954--960}
}

@ARTICLE{Mom+95,
  author = {J.C.M. Mombach and J.A. Glazier and R.C. Raphael and M. Zajac},
  title = {Quantitative comparison between differential adhesion models and
	cell sorting in the presence and absence of fluctuations},
  journal = {Phys. Rev. Lett.},
  year = {1995},
  volume = {75},
  pages = {2244--2247}
}

@ARTICLE{MONS95,
  author = {R. Monshouwer and I.O. de Zarate and F. van Mourik and R. van Grondelle},
  title = {Low-intensity oumb--probe spectroscopy on the B800 to B850 transfer
	in the light harvesting 2 complex of {\em {R}hodobacter spharoides}},
  journal = {Chem.~Phys.~Lett.},
  year = {1995},
  volume = {246},
  pages = {341--346}
}

@PHDTHESIS{Muru95,
  author = {A. Murua},
  title = {M\'etodos Simpl\'ecticos Desarrollables in P-series},
  school = {Universidad de Valladolid},
  year = {1995}
}

@ARTICLE{MYMR95,
  author = {J.~S.~Mymryk and T.~K.~Archer},
  title = {Dissection of progesterone receptor-mediated chromatin remodeling
	and transcriptional activation in vivo},
  journal = GAD,
  year = {1995},
  volume = {9},
  pages = {1366--1376}
}

@ARTICLE{MYMR95A,
  author = {J.~S.~Mymryk and D.~Bernard and G.~L.~Hager and T.~K.~Archer},
  title = {Mouse mammary tumor virus chromatin in human breast cancer cells
	is constitutively hypersensitive and exhibits steroid hormone-independent
	loading of transcription factors in vivo},
  journal = MCB,
  year = {1995},
  volume = {15},
  pages = {26--34},
  number = {1}
}

@INCOLLECTION{MULL95,
  author = {K.-R. M{\"u}ller and M. Finke and N. Murata and K. Schulten and S.
	Amari},
  title = {Large Scale Simulations for Learning Curves},
  booktitle = {Progress in neural Processing Vol. {\bf 1} / Neural Networks: The
	Statistical Mechanics Perspective},
  publisher = {World Scientific},
  year = {1995},
  editor = {Jong-Hoon Oh and Chulan Kwon and Sungzoon Cho},
  pages = {73--84},
  address = {Singapore}
}

@ARTICLE{MULL95A,
  author = {K.-R. M{\"u}ller and N. Murata and M. Finke and K. Schulten and S.
	Amari},
  title = {A Numerical Study of Learning Curves in Stochastic Multi-Layer Feed-Forward
	Networks},
  journal = NC,
  year = {1995},
  volume = {8},
  pages = {1085--1106},
  annote = {[University of Tokyo Technical Report METR 95-03]}
}

@ARTICLE{NASS95,
  author = {Nicolas Nassar and Gudrun Horn and Christian Herrmann and Anna Scherer
	and Frank McCormick and Alfred Wittinghofer},
  title = {The 2.2\,{\AA} crystal structure of the Ras-binding domain of the
	serine/threonine kinase c-{Raf1} in complex with {Rap1A} and a {GTP}
	analogue},
  journal = NAT,
  year = {1995},
  volume = {375},
  pages = {554--560}
}

@INPROCEEDINGS{NELS95,
  author = {M. Nelson and W. Humphrey and A. Gursoy and A. Dalke and L. Kal{\'e}
	and R. Skeel and K. Schulten and R. Kufrin},
  title = {{MDScope} -- A Visual Computing Environment for Structural Biology},
  booktitle = {Computational Mechanics 95},
  year = {1995},
  editor = {S.N. Atluri and G. Yagawa and T.A. Cruse},
  volume = {1},
  pages = {476--481}
}

@ARTICLE{NELS95A,
  author = {M. Nelson and W. Humphrey and A. Gursoy and A. Dalke and L. Kal{\'e}
	and R.~D. Skeel and K. Schulten and R. Kufrin},
  title = {{MDScope} -- A Visual Computing Environment for Structural Biology},
  journal = CPC,
  year = {1995},
  volume = {91},
  pages = {111--134},
  number = {1, 2 and 3},
  annote = {[Beckman Institute Technical Report TB-94-18]},
  tbtechrep = {TB-94-18}
}

@ARTICLE{NHGD95a,
  author = {M. Nelson and W. Humphrey and A. Gursoy and A. Dalke and L. Kal{\'e}
	and R.~D. Skeel and K. Schulten and R. Kufrin},
  title = {{MDScope}---A Visual Computing Environment for Structural Biology},
  journal = {Comput.\ Phys.\ Commun.},
  year = {1995},
  volume = {91},
  pages = {111--134},
  number = {1, 2 and 3},
  ack = {NIH, GC},
  nremark = {[Beckman Institute Technical Report TB-94-18]}
}

@INPROCEEDINGS{NHGD95b,
  author = {M. Nelson and W. Humphrey and A. Gursoy and A. Dalke and L. Kal{\'e}
	and R.~D. Skeel and K. Schulten and R. Kufrin},
  title = {{MDScope}--- A Visual Computing Environment for Structural Biology},
  booktitle = {{ICES '95} Conference Proceedings---Computational Mechanics 95},
  year = {1995},
  editor = {S.N. Atluri and G. Yagawa and T.A. Cruse},
  volume = {1},
  pages = {476--481},
  nremark = {a shortened version of the CPC paper for a conference, organized by
	A. Sameh and others, that KS is invited to. It is a 6 page version
	of the CPC paper, all text taken straight from the CPC paper, with
	no figures.}
}

@ARTICLE{NICH95,
  author = {William L. Nichols and George Rose and Lynn F. Ten Eyck and Bruno
	H. Zimm},
  title = {Rigid Domains in Proteins: An Algorithmic Approach to Their Identification},
  journal = PSFG,
  year = {1995},
  volume = {23},
  pages = {38--48}
}

@ARTICLE{NINA95,
  author = {M. Nina and B. Roux and J. Smith},
  title = {Functional Interactions in Bacteriorhodopsin: A Theoretical Analysis
	of Retinal Hydrogen Bonding with Water},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {25--39}
}

@ARTICLE{OBRI95,
  author = {Melanie C. O'Brien and David B. McKay},
  title = {How Potassium Affects the Activity of the Molecular Chaperone {H}sc70},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {2247--2250}
}

@ARTICLE{OHKA95,
  author = {H. Ohkawa and others},
  title = {{MMDB}: an {ASN}.1 specification for macromolecular structure},
  journal = {Ismb},
  year = {1995},
  volume = {3},
  pages = {259--267}
}

@ARTICLE{ONG95A,
  author = {S. Ong and H. Liu and X. Qiu and G. Bhat and C. Pidgeon},
  title = {Membrane Partition Coefficients Chromotographically Measured Using
	Immobilized Artificial Membrane Surfaces},
  journal = {Analytical Chemistry},
  year = {1995},
  volume = {67},
  pages = {755--762}
}

@ARTICLE{ONG95,
  author = {S. Ong and C. Pidgeon},
  title = {Thermodynamics of Solute Partitioning into Immobilized Artificial
	Membranes},
  journal = {Analytical Chemistry},
  year = {1995},
  volume = {67},
  pages = {2119--2128}
}

@ARTICLE{ORLO95,
  author = {A. Orlova and E. H. Egelman},
  title = {Structural Dynamics of {F}-actin: {I.} Changes in the {C} terminus},
  journal = JMB,
  year = {1995},
  volume = {245},
  pages = {582--597}
}

@ARTICLE{ORLO95A,
  author = {A. Orlova and E. Prochniewicz and E. H. Egelman},
  title = {Structural Dynamics of {F}-actin: {II.} Cooperativity in Structural
	Transitions},
  journal = JMB,
  year = {1995},
  volume = {245},
  pages = {598--607}
}

@ARTICLE{OTTO95,
  author = {James C. Otto and William L. Smith},
  title = {Prostaglandin endoperoxide synthase-1 and -2},
  journal = JLMCS,
  year = {1995},
  volume = {12},
  pages = {139--156}
}

@ARTICLE{PERE95,
  author = {Irina Perelroizen and Marie-France Carlier and Dominique Pantaloni},
  title = {Binding of Divalent Cation and Nucleotide to {G}-actin in the presence
	of Profilin},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {1501--1508}
}

@ARTICLE{PeEB95,
  author = {L. Perera and U. Essmann and M. L. Berkowitz},
  title = {{E}ffect of the treatment of long-range forces on the dynamics of
	ions in aqueous solutions},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {102},
  pages = {450}
}

@ARTICLE{Pete95,
  author = {H. G. Petersen},
  title = {Accuracy and efficiency of the particle mesh {E}wald method},
  journal = JCP,
  year = {1995},
  volume = {103},
  number = {3668--3679},
  annote = {In this article, a recently proposed method called the particle mesh
	Ewald ~PME! method for computing the long ranged Coulomb interactions
	in for example molecular dynamics simulations is studied. The PME
	method has a complexity O~N log N!, where N is the total number of
	charges. This complexity should in particular be compared with the
	complexity O~N 3/2 ! for the well known Ewald method and O(N) for
	the rather new ~but already famous! fast multipole method ~FMM!.
	However, these complexities say nothing about which method is fastest
	at some finite N. The purpose of this article is thus to study the
	PME method and compare its efficiency with the Ewald method and the
	fast multipole method. To enable this, a theoretical estimate for
	the accuracy of the PME method as function of its truncation parameters
	is derived. It is shown that this estimate is very precise by comparing
	it with results obtained from molecular dynamics simulations of a
	molten NaCl. Based on this estimate and very careful time experiments,
	the overall necessary time overhead for the PME method as function
	of N and a required accuracy is predicted. By a direct comparison
	with a similar prediction for the Ewald method and by studying existing
	Ewald-FMM comparisons, it is found that the PME method is significantly
	faster than both the Ewald method and the fast multipole method in
	the important decades N.10 4 -10 5 .(c) 1995 American Institute of
	Physics.}
}

@ARTICLE{PFUH95A,
  author = {M. Pfuhl and M. Gautel and A. Politou and C. Joseph and A. Pastore},
  title = {Secondary structure determination by {N}{M}{R} spectroscopy of an
	immunoglobulin-like domain from the giant muscle protein titin},
  journal = JBNMR,
  year = {1995},
  volume = {5},
  pages = {48--58}
}

@ARTICLE{PFUH95,
  author = {M. Pfuhl and A. Pastore},
  title = {Tertiary structure of an immunoglobulin-like domain fron the giant
	muscle protein titin: a new member of the {I} set},
  journal = STR,
  year = {1995},
  volume = {3},
  pages = {391--401}
}

@ARTICLE{PHIL95B,
  author = {M.~Philippopoulos and C.~Lim},
  title = {Molecular dynamics simulation of {\em E.coli} ribonuclease H$_1$
	in solution: correlation with {NMR} and X-Ray data and insights into
	biological function.},
  journal = JMB,
  year = {1995},
  volume = {254},
  pages = {771--792}
}

@INCOLLECTION{PHIL95,
  author = {James Phillips and Klaus Schulten},
  title = {Modeling {AFM} Tip Dynamics Through Diffusion in Time-Periodic Potentials},
  booktitle = {NATO Advanced Research Workshop on Atomic Force Microscopy},
  publisher = {Kluwer Academic Publishers},
  year = {1995},
  editor = {J. Rabe},
  series = {NASD},
  address = {New York},
  note = {In press. [Beckman Institute Technical Report TB-95-03]},
  tbtechrep = {TB-95-03}
}

@ARTICLE{PHIL95A,
  author = {James Phillips and Klaus Schulten},
  title = {Diffusive hysteresis at high and low driving frequencies},
  journal = PRE,
  year = {1995},
  volume = {52},
  pages = {2473--2477},
  number = {3}
}

@ARTICLE{PIDG95,
  author = {C. Pidgeon},
  title = {{IAM} Chromatography: {A}n {\em in Vitro} Screen for Predicting Drug
	Membrane Permeability},
  journal = {Journal of Medicinal Chemistry},
  year = {1995},
  volume = {38},
  pages = {590--594}
}

@ARTICLE{PIED95,
  author = {F.~J.~Piedrafita and I.~Bendik and M.~A.~Ortiz and M.~Pfahl},
  title = {Thyroid hormone receptor homodimers can function as ligand--sensitive
	repressors.},
  journal = {Mol.End.},
  year = {1995},
  volume = {9},
  pages = {563--578}
}

@ARTICLE{Plim95,
  author = {S. Plimpton},
  title = {Fast Parallel Algorithms for Short-Range Molecular Dynamics},
  journal = JCP,
  year = {1995},
  volume = {117},
  pages = {1--19},
  annote = {LAMMPS}
}

@ARTICLE{POLA95,
  author = {K.~J.~Polach and J.~Widom},
  title = {Mechanism of Protein Access to Speific {DNA} Sequences in Chromatin:
	A Dynamic Equilibrium Model for Gene Regulation},
  journal = JMB,
  year = {1995},
  volume = {254},
  pages = {130--149},
  number = {2}
}

@ARTICLE{POLI95,
  author = {A. S. Politou and D. Thomas and A. Pastore},
  title = {The folding and the stability of titin immunoglobulin-like modules,
	with implications for mechanism of elasticity},
  journal = BJ,
  year = {1995},
  volume = {69},
  pages = {2601--2610}
}

@ARTICLE{POME95,
  author = {R. Pom{\`e}s and R. C. Willson and J. A. McCammon},
  title = {Free Energy Simulations of the {H}y{HEL}-10/{HEL} Antibody-Antigen
	Complex},
  journal = {Protein Engineering},
  year = {1995},
  volume = {3},
  pages = {663--675},
  number = {7}
}

@ARTICLE{PoSa95,
  author = {A. Portillo and J.~M. Sanz-Serna},
  title = {Lack of dissipativity is not symplecticness},
  journal = {BIT Numer.\ Math.},
  year = {1995},
  volume = {35},
  pages = {269--276},
  number = {2}
}

@ARTICLE{PRED95,
  author = {P.~F.~Predki and B.~Sarkar},
  title = {Cooperative interaction of oestrogen receptor 'zinc finger' domain
	polypeptides on {DNA} binding.},
  journal = BCHJ,
  year = {1995},
  volume = {305},
  pages = {805--810},
  annote = {studies of ER dimer binding to a GRE-ERE sequence}
}

@ARTICLE{Prin95,
  author = {G. J. Pringle},
  title = {Embedding a `{T}reecode' on a {MIMD} Parallel Computer Using a Domain
	Decomposition Paradigm},
  journal = {Future Gener. Comput. Syst.},
  year = {1995},
  volume = {11}
}

@ARTICLE{Quis95,
  author = {G. R. W. Quispel},
  title = {Volume-Preserving Integrators},
  journal = {Physics Letters A},
  year = {1995},
  volume = {206},
  pages = {26--30},
  number = {1 and 2}
}

@ARTICLE{Rama95,
  author = {G. Ramaswami},
  title = {Perturbed Collocation and Symplectic {RKN} Methods},
  journal = {Advances in Computational Mathematics},
  year = {1995},
  volume = {3},
  pages = {23--40},
  number = {I-II}
}

@ARTICLE{RaBo95,
  author = {W. Rankin and J. Board},
  title = {A Portable Distributed Implementation of the Parallel Multipole Tree
	Algorithm},
  journal = {IEEE Symposium on High Performance Distributed Computing},
  year = {1995},
  note = {[Duke University Technical Report 95-002]}
}

@ARTICLE{RANK95,
  author = {W. Rankin and J. Board},
  title = {A Portable Distributed Implementation of the Parallel Multipole Tree
	Algorithm},
  journal = {IEEE Symposium on High Performance Distributed Computing},
  year = {1995},
  note = {In press. [Duke University Technical Report 95-002]}
}

@BOOK{Rapa95,
  title = {The Art of Molecular Dynamics Simulation},
  publisher = {Cambridge University Press},
  year = {1995},
  author = {D.~C. Rapaport}
}

@ARTICLE{RAST95,
  author = {F.~Rastinejad and T.~Perlmann and R.~M.~Evans and P.~Sigler},
  title = {Structural determinants of nuclear receptor assembly on {DNA} direct
	repeats.},
  journal = NAT,
  year = {1995},
  volume = {375},
  pages = {203--211},
  annote = {studies of ER dimer binding to a GRE sequence without any spacer
	base-pairs between the half sites.}
}

@INCOLLECTION{READ95,
  author = {C. M. Read and P. D. Cary and C. Crane-Robinson and P. C. Driscoll
	and M. O. M. Carillo and D. G. Norman},
  title = {The Structure of the {HMG} Box and its Interactions with {DNA}},
  booktitle = {Nucleic Acids and Molecular Biology},
  publisher = {Springer-Verlag},
  year = {1995},
  editor = {F. Ekstein and D. M. J. Lilley},
  pages = {222--250},
  address = {Berlin}
}

@ARTICLE{Reic95,
  author = {S. Reich},
  title = {Smoothed Dynamics of Highly Oscillatory {H}amiltonian Systems},
  journal = {Physica D},
  year = {1995},
  volume = {89},
  pages = {28--42},
  number = {1 and ~2},
  nack = {doe/nsf, nsf/arpa gcag, nih},
  nremark = {also Reich, S., Molecular dynamics with soft constraints, Technical
	Report UIUC-BI-TB-94-12, Beckman Institute, Urbana, 1994.}
}

@ARTICLE{REIC95d,
  author = {S. Reich},
  title = {Enhancing Energy Conserving Methods},
  year = {1995},
  note = {Submitted to BIT}
}

@ARTICLE{RENA95,
  author = {J.~P.~Renaud and N.~Rochel and M. Ruff and V.~Vivat and P.~Chambon
	and H.~Gronemeyer and D.~Moras},
  title = {Crystal structure of the {RAR}-${\gamma}$ ligand--binding domain
	bound to all--{\em trans} retinoic acid.},
  journal = Nat,
  year = {1995},
  volume = {378},
  pages = {681--689},
  annote = {2A resolution}
}

@ARTICLE{RENT95,
  author = {Robert Renthal and Kirk McMillan and Leticia Guerra and Margot N.
	Garcia and Roy Rangel and Chih-Min Jen},
  title = {Long-Range Effects on the Retinal Chromophore of Bacteriorhodopsin
	Caused by Surface Carboxyl Group Modification},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {7869--7878}
}

@ARTICLE{REYN95,
  author = {J. Reynders and D. Forslund and P. Hinker and M. Tholburn and D.
	Kilman and W. Humphrey},
  title = {{OOPS} - An Object-Oriented Particle Simulation Class Library for
	Distributed Architectures},
  journal = CPC,
  year = {1995},
  volume = {87},
  pages = {212--222}
}

@ARTICLE{RIBE95,
  author = {R.~C.~J.~Ribeiro and P.~J.~Kushner and J.~D.~Baxter},
  title = {The nuclear hormone receptor gene superfamily.},
  journal = ARM,
  year = {1995},
  volume = {46},
  pages = {443--453}
}

@ARTICLE{ROBE95A,
  author = {J. E. Roberts and J. Schnitker},
  title = {Boundary Conditions in Simulations of Aqueous Ionic Solutions: A
	Systematic Study},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {1322--1331}
}

@ARTICLE{ROBE95,
  author = {M.~S.~Roberts and G.~Gragoso and G.~L.~Hager},
  title = {Nucleosomes reconstituted {\it in vitro} on mouse mammary tumor virus
	{B} region {DNA} occupy multiple translational and rotational frames},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {12470--12480}
}

@ARTICLE{ROMO95,
  author = {T. D. Romo and J. B. Clarage and D. C. Sorensen and G. N. Phillips
	Jr.},
  title = {Automatic identification of discrete substates in proteins: singular
	value decomposition analysis of time-averaged crystallographic refinements},
  journal = PRO,
  year = {1995},
  volume = {22},
  pages = {311--321}
}

@ARTICLE{ROUS95,
  author = {Itay Rousso and Igor Brodsky and Aaron Lewis and Mordechai Sheves},
  title = {The Role of Water in Retinal Complexation to Bacterio-opsin},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {13860--13868},
  annote = {spectroscopic evidence of need for water and roles}
}

@ARTICLE{ROUX95,
  author = {Benoit Roux},
  title = {The calculation of the potential of mean force using computer simulations},
  journal = {Computer Physics Communications},
  year = {1995},
  volume = {91},
  pages = {275--282}
}

@ARTICLE{ROUX95A,
  author = {B.~Roux and M.~Karplus},
  title = {Potential energy function for cation-peptide interactions -- an ab
	initio study},
  journal = JCC,
  year = {1995},
  volume = {16},
  pages = {690--704},
  number = {6},
  annote = {Main result is that you need ion-induced polarization to do ion-peptide
	interactions correctly.}
}

@ARTICLE{SABL95,
  author = {E.P. Sablin and R.J. Fletterick},
  title = {Crystallization and Preliminary Structural Studies of the ncd motor
	domain},
  journal = PRO,
  year = {1995},
  volume = {21},
  pages = {68--69}
}

@ARTICLE{SAND95,
  author = {Bilha Sandak and Ruth Nussinov and Haim J. Wolfson},
  title = {An automated computer vision and robotics-based technique for {3-D}
	flexible biomolecular docking and matching},
  journal = {Comp. Appl. Biosciences},
  year = {1995},
  volume = {11},
  pages = {87--99}
}

@TECHREPORT{SaAM95,
  author = {J. M. Sanz-Serna and Araujo and Murua},
  title = {Symplectic methods based on decompositions},
  institution = {Universidad de Valladolid},
  year = {1995},
  address = {Valladolid, Spain}
}

@ARTICLE{SCHA95,
  author = {C. Scharnagl and J. Hettenkofer and S. Fisher},
  title = {Electrostatic and Conformational Effects on the Proton Translocation
	Steps in Bacteriorhodopsin: Analysis of Multiple {M} Structures},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {7787--7800}
}

@ARTICLE{SCHE95,
  author = {R.W. Schevitz and N.J. Bach and D.G. Carlson and N.Y. Chirgadze and
	D.K. Clawson and R.D. Dillard and S.E. Draheim and L.W. Hartley and
	N.D. Jones and E.D. Mihelich and J.L. Olkowski and D.W. Snyder and
	C. Sommers and J.P. Wery},
  title = {STRUCTURE-BASED DESIGN OF THE FIRST POTENT AND SELECTIVE INHIBITOR
	OF HUMAN NON-PANCREATIC SECRETORY PHOSPHOLIPASE {A}$_2$},
  journal = NATSB,
  year = {1995},
  volume = {2},
  pages = {458--465},
  annote = {Lilly paper on PLA2 drug design}
}

@ARTICLE{SCHL95,
  author = {Tamar Schlick},
  title = {Modeling superhelical {DNA}: recent analytical and dynamic approaches},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {245--262}
}

@ARTICLE{SCHN95,
  author = {B.~Schneider and H.~M.Berman.},
  title = {Hydration of the {DNA} bases is local},
  journal = BJ,
  year = {1995},
  volume = {69},
  pages = {2661--2669}
}

@ARTICLE{SCHO95,
  author = {G. Scholes and R. Harcourt and K. Ghiggino},
  title = {Rate expressions for excitation transfer. An ab inition study of
	electronic factors in excitation transfer and exciton resonance interactions},
  journal = JCP,
  year = {1995},
  volume = {102},
  pages = {7302--7312}
}

@INPROCEEDINGS{SCHU95,
  author = {Klaus Schulten},
  title = {Curve Crossing in a Protein: Coupling of the Elementary Quantum Process
	to Motions of the Protein},
  booktitle = {Proceedings of the Ecole de Physique des Houches},
  year = {1995},
  editor = {D. Bicout and M. J. Field},
  pages = {85--118},
  address = {Paris},
  publisher = {Les Editions de Physique, Springer}
}

@ARTICLE{SCHU95B,
  author = {Klaus Schulten and William Humphrey and Ilya Logunov and Mordechai
	Sheves and Dong Xu},
  title = {Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles},
  journal = IJC,
  year = {1995},
  volume = {35},
  pages = {447--464},
  annote = {Invited publication.}
}

@ARTICLE{SCHU95Z,
  author = {C. E. Schutt and M. D. Rozycki and J. C. Myslik and U. Lindberg},
  title = {A discourse on modeling {F}-actin},
  journal = JSB,
  year = {1995},
  volume = {115},
  pages = {186--198}
}

@ARTICLE{SCHW95,
  author = {J.~W.~R.~Schwabe and L.~C.~Chapman and D.~Rhodes},
  title = {The oestrogen receptor recognizes an imperfectly palindromic response
	element through an alternative side-chain conformation},
  journal = STR,
  year = {1995},
  volume = {3},
  pages = {201--213},
  annote = {shows that recognition of the non-consensus sequence, one base-pair
	different, is achived by the rearrangement of Lys28}
}

@ARTICLE{SEGN95,
  author = {B.~Segnitz and U.~Gehring},
  title = {Subunit structure of the nonactivated human estrogen receptor},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {2179--2183}
}

@ARTICLE{SHAR95,
  author = {K.~A.~Sharp and B.~Honig},
  title = {Salt effects on nucleic acids.},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {323--328}
}

@ARTICLE{SHEN95,
  author = {Qing Sheng and Klaus Schulten and Charles Pidgeon},
  title = {A Molecular Dynamics Simulation of Immobilized Artificial Membranes},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {11018--11027},
  number = {27},
  annote = {[Beckman Institute Technical Report TB-95-04]}
}

@ARTICLE{SHIM95,
  author = {T. Shimizu and E. Sablin and R.D. Vale and R. Fletterick and E. Pechatnikova
	and E.W. Taylor},
  title = {Expression, purification, {ATP}ase properties, and microtubule-binding
	properties of the ncd motor domain},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {13259--13266}
}

@ARTICLE{SiHQ95,
  author = {S. Sigurdsson and L. Hernquist and G. D. Quinlan},
  title = {Models of Galaxies with Central Black Holes---Simulation Methods},
  journal = {ASTROPHYSICAL-JOURNAL},
  year = {1995},
  volume = {446},
  pages = {75--85},
  number = {1}
}

@ARTICLE{SIMO95,
  author = {Thomas Simonson and David Perahia},
  title = {Internal and Interfacial Dielectric Properties of Cytochrome c from
	Molecular Dynamics in Aqueous Solution},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {1082--1086}
}

@ARTICLE{SING95,
  author = {J. P. Singh and C. Holta and T. Totsuka and A. Gupta and J. Hennessy},
  title = {Load Balancing And Data Locality In Adaptive Hierarchical {N}-Body
	Methods - {B}arnes-{H}ut, {F}ast {M}ultipole and {R}adiosity},
  journal = JPDC,
  year = {1995},
  volume = {27},
  pages = {118--141},
  number = {2}
}

@ARTICLE{SIPP95,
  author = {M. Sippl},
  title = {Knowledge-based Potentials for Proteins},
  journal = COSB,
  year = {1995},
  volume = {5},
  pages = {229--235}
}

@ARTICLE{SIVO95,
  author = {A.~V.~Sivolob and S.~N.~Khrapunov},
  title = {Translational positioning of nucleosomes on {DNA}: the role of sequence
	dependent isotropic {DNA} bending stiffness},
  journal = JMB,
  year = {1995},
  volume = {247},
  pages = {918--931}
}

@ARTICLE{Skee95,
  author = {R.~D. Skeel},
  title = {Numerical {H}amiltonian {P}roblems ({J}. {M}. {S}anz-{S}erna and
	{M}. {P}. {C}alvo)},
  journal = {SIAM Review},
  year = {1995},
  volume = {37},
  number = {2}
}

@ARTICLE{SLUP95,
  author = {C.M. Slupsky and B.D. Sykes},
  title = {{NMR} Solution Structure of Calcium-Saturated Skeletal Muscle Troponin
	{C}},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {15953--15964}
}

@ARTICLE{SMAL95,
  author = {G. J. Small},
  title = {On the validity of the standard model for primary charge separation
	in the bacterial reaction center},
  journal = CP,
  year = {1995},
  volume = {197},
  pages = {239-257}
}

@ARTICLE{SMIT95,
  author = {C.A. Smith and I. Rayment},
  title = {{X}-ray structure of the Magnesium(II)-Pyrophosphate Complex of the
	Truncated Head of {{\em Dictyostelium discoideum}} Myosin to 2.5\,{{\AA}}
	Resolution},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {8973--8981}
}

@ARTICLE{SmPe95,
  author = {P. E. Smith and B. M. Pettitt},
  title = {Efficient {E}wald Electrostatic Calculations for Large Systems},
  journal = CPC,
  year = {1995},
  volume = {91},
  pages = {339--344},
  number = {1}
}

@ARTICLE{SSSW95,
  author = {Paul E. Smith and Rene C. van Schaik and Thomas Szyperski and Kurt
	Wuthrich and Wilfred F. van Gunsteren},
  title = {Internal Mobility of the Basic Pancreatic Trypsin Inhibitor in Solution:
	A comparison of NMR Spin Relaxation Measurements and Molecular Dynamics
	Simulations},
  journal = JMB,
  year = {1995},
  volume = {246},
  pages = {356--365}
}

@ARTICLE{SMIT95A,
  author = {William L. Smith and David L. DeWitt},
  title = {Biochemistry of Prostaglandin {H} Synthase-1 and Synthase-2 and Their
	Differential Susceptibility to Nonsteroidal Anti-Inflammatory Drugs},
  journal = SIN,
  year = {1995},
  volume = {15},
  pages = {179--194},
  number = {3}
}

@ARTICLE{SKPP95,
  author = {D. Solvason and J. Kolafa and H. G. Petersen and J. W. Perram},
  title = {A rigorous comparison of the {E}wald method and the fast multipole
	method in 2 dimensions},
  journal = {Comp. Phys. Comm.},
  year = {1995},
  volume = {87},
  pages = {307--318}
}

@ARTICLE{STAN95,
  author = {R. J. Stanley and S. G. Boxer},
  title = {Oscillations in the Spontaneous Fluorescence from Photosynthetic
	Reaction Centers},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {859--863}
}

@BOOK{STRY95,
  title = {Biochemistry},
  publisher = {W. H. Freeman and Company},
  year = {1995},
  author = {L. Stryer},
  address = {New York},
  edition = {4th}
}

@ARTICLE{SUTT95,
  author = {R. Brayn Sutton and Razbek A. Davletov and Albert M. Berghuis and
	Thomas C. Sudhof and Stephen R. Sprang},
  title = {Structure of the first {C}2 domain of synaptotagmin {I}: A novel
	{Ca}2+/phospholipid-binding fold},
  journal = {Cell},
  year = {1995},
  volume = {80},
  pages = {929--938}
}

@ARTICLE{SWAM95,
  author = {Musti J. Swamy},
  title = {Thermodynamic Analysis of Biotin Binding to Avidin. {A} High Sensitivity
	Titration Calorimetric Study},
  journal = BCHMBI,
  year = {1995},
  volume = {36},
  pages = {219--225},
  annote = {june 1}
}

@ARTICLE{TEO95,
  author = {S.-H. Teo and K. D. Grasser and C. H. Hardman and R. W. Broadhurst
	and E. D. Laue and J. O. Thomas},
  title = {Two mutations in the {HMG-box} with very different structural consequences
	provide insights into the nature of binding to four-way junction
	{DNA}},
  journal = EMBO,
  year = {1995},
  volume = {14},
  pages = {3844--3853},
  number = {15}
}

@ARTICLE{THOM95,
  author = {M. Thompson and G. Schenter},
  title = {Excited States of the Bacteriochlorophyll b Dimer of {\it Rhodopseudomanas
	viridus}: A {QM/MM} Study of the Photosynthetic Reaction Center That
	Induces {MM} Polarization},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {6374--6386}
}

@ARTICLE{TIMP95,
  author = {K. Timpmann and A. Freiberg and V. Sundstrom},
  title = {Energy trapping and detrapping in the photosynthetic bacterium {\em
	Rhodopseudomonas viridis}: transfer-to-trap-limited dynamics},
  journal = CP,
  year = {1995},
  volume = {194},
  pages = {275--283}
}

@ARTICLE{TIRI95,
  author = {M. M. Tirion and D. {ben-Avraham} and M. Lorenz and K. C. Holmes},
  title = {Normal Modes as Refinement Parameters for the {F}-Actin Model},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {5--12}
}

@ARTICLE{TITT95,
  author = {J. Tittor and D. Oesterhelt and E. Bamberg},
  title = {Bacteriorhodopsin Mutants {D85N}, {D85T}, and {D85,96N} as Proton
	Pumps},
  journal = BPC,
  year = {1995},
  volume = {56},
  pages = {153--157}
}

@ARTICLE{TONG95,
  author = {G.~X.~Tong and M.~R.~Tanen and M.~K.~Bagchi},
  title = {Ligand modulates the interaction of thyroid hormone receptor $\beta$
	with the basal transcription machinery.},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {10601--10611},
  annote = {on the web}
}

@ARTICLE{Toxv95,
  author = {S{\o}ren Toxvaerd},
  title = {Hamiltonians for Discrete Dynamics},
  journal = {Phys.\ Rev.\ E},
  year = {1995},
  nremark = {June 11, 1994; 7 pages}
}

@ARTICLE{TRUS95,
  author = {M.~Truss and J.~Bartsch and A.~Schelbert and R.~J.~G.~Hach{\'e} and
	M.~Beato},
  title = {Hormone induces binding of receptors and transcription factors to
	a rearranged nucleosome on the {MMTV} promoter {\it in vivo}},
  journal = EMBO,
  year = {1995},
  volume = {14},
  pages = {1737--1751},
  number = {8}
}

@ARTICLE{TSAI95,
  author = {A.~Tsai and R.J.~Kulmacz and G.~Palmer},
  title = {{Spectroscopic evidence for reaction of prostaglandin H synthase-1
	tyrosyl radical with arachidonic acid}},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {10503--10508},
  number = {18}
}

@ARTICLE{TSUK95,
  author = {T.\ Tsukihara and H.\ Aoyama and E.\ Yamashita and T.\ Tomizaki and
	H.\ Yamaguchi and K.\ Shinnzawha-Itoh and R.\ Nakashima and R.\ Yaono
	and S.\ Yoshikawa},
  title = {Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase
	at 2.8 {{\AA}}},
  journal = SCI,
  year = {1995},
  volume = {269},
  pages = {1069--1074}
}

@ARTICLE{TURN95,
  author = {James Turner and Paul Weiner and Barry Robson and Ravi Venugopal
	and Harry {Schubele~{III}} and Ramen Singh},
  title = {Reduced Variable Molecular Dynamics},
  journal = JCC,
  year = {1995},
  volume = {16},
  pages = {1271--1290},
  number = {10}
}

@INPROCEEDINGS{TZON95,
  author = {Svilen Tzonev and Joseph Malpeli and Klaus Schulten},
  title = {Morphogenesis of the Lateral Geniculate Nucleus: How Singularities
	Affect Global Structure},
  booktitle = {Advances in Neural Information Processing Systems 7},
  year = {1995},
  editor = {G. Tesauro and D. Touretzky and T. Leen},
  pages = {133--140},
  address = {Cambridge, Mass and London, England},
  publisher = {MIT Press},
  techrep = {TB-94-13}
}

@ARTICLE{HOUT95,
  author = {L. P. A. {Van Houte} and V. P. Chuprina and M. {van de Wetering}
	and R. Boelens and R. Kaptein and H. Clevers},
  title = {Solution Structure of the Sequence-Specific {HMG} box of the Lymphocyte
	Transcriptional Activator {Sox-4}},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {30516--30524}
}

@ARTICLE{ViMe95,
  author = {J. Vincent and K.~M. Merz},
  title = {A highly portable parallel implementation of {AMBER} using the {M}essage
	{P}assing {I}nterface standard},
  journal = JCC,
  year = {1995},
  volume = {11},
  pages = {1420--1427}
}

@ARTICLE{VISS95,
  author = {R. W. Visschers and L. Germeroth and H. Michel and R. Monshouwer
	and R. {van Grondelle}},
  title = {Spectroscopic properties of the light-harvesting complexes from {{\em
	{R}hodospirillum molischianum}}},
  journal = BBA,
  year = {1995},
  volume = {1230},
  pages = {147--154}
}

@ARTICLE{VADM95,
  author = {M. Viswanathan and J. M. Anchin and P. R. Droupadi and C. Mandal
	and D. S. Linthicum and S. Subramaniam},
  title = {Structural Predictions of the Binding Site Architecture for Monoclonial
	Antibody {NC}6.8 Using Ligand Binding, Spectroscopy and Computer-Aided
	Molecular Modeling},
  journal = {Bioph.\ J.},
  year = {1995},
  volume = {69},
  pages = {741--753}
}

@ARTICLE{Vote95,
  author = {A.~F.~Voter},
  title = {The Embedded Atom method},
  journal = {Inter-metallic Compounds:Principles and Practice, edited by J.~H.~Westbrook
	and R.~L.~Fleisher, John Wiley and Sons Ltd.},
  year = {1995},
  volume = {1},
  pages = {77}
}

@ARTICLE{WAGN95,
  author = {R.~Wagner and J.~W.~Apriletti and M.~E.~McGrath and B.~L.~West and
	J.~D.~Baxter and R.~J.~Fletterick},
  title = {A structural role for hormone in the thyroid hormone receptor.},
  journal = Nat,
  year = {1995},
  volume = {378},
  pages = {690--697},
  annote = {in press}
}

@ARTICLE{WANG95A,
  author = {J.H. Wang and R.B. Pepinsky and T. Stehle and J.H. Liu and M. Karpusas
	and B. Browning and L. Osborn},
  title = {The crystal structure of an {N}-terminal two-domain fragment of vascular
	cell adhesion molecule 1 (VCAM-1)},
  journal = PNAS,
  year = {1995},
  pages = {5714},
  volumn = {92}
}

@ARTICLE{WZWS95,
  author = {Y. Wang and H. Zhang and L. Wei and R. Scott},
  title = {Discriminating Compact Nonative Structures from the Native Structure
	of Globular Proteins},
  journal = PNAS,
  year = {1995},
  volume = {92},
  pages = {709--713}
}




@ARTICLE{WaSa95,
  author = {M. S. Warren and J. K. Salmon},
  title = {A Portable Parallel Particle Program},
  journal = CPC,
  year = {1995},
  volume = {87},
  pages = {266--290},
  number = {1-2}
}

@ARTICLE{WaKa95,
  author = {Masakatsu Watanabe and Martin Karplus},
  title = {Simulation of Macromolecules by Multiple-Time-Step Methods},
  journal = {J. Phys.\ Chem.},
  year = {1995},
  volume = {99},
  pages = {5680--5697},
  number = {15},
  nabstract = {Molecular dynamics simulations of macromolecules require long computation
	times to generate the trajectories needed for determining their thermodynamic
	and dynamic properties. The most rapidly varying quantities, such
	as the bond lengths, limit the integration time step, while the more
	slowly varying molecular processes are of primary interest. The form
	of the empirical potential energy function used in simulations of
	macromolecules makes it possible to exploit the existing separation
	of time scales by use of the reversible multiple time-step method
	(Tuckerman, Berne, and Martyna. J. Chem. Phys. 1992, 97, 1990). Implementation
	of the method in Cartesian coordinates yields an efficient multiple
	time-step algorithm for molecular dynamics with a velocity Verlet
	integrator. The forces acting on individual atoms are classified
	as hard, medium, and soft; for example, hard forces are contributed
	by bond-stretching and bond-angle bending terms, medium forces by
	dihedral angle and nonbonded (van der Waals and electrostatic) interaction
	terms acting on hydrogen atoms, and soft forces by the remaining
	nonbonded interaction terms. The multiple time-step approach is tested
	in short (10 ps) simulations of the pentapeptide Met-enkephalin and
	the protein the bovine pancreatic trypsin inhibitor. The stability
	of the integration methods and the dynamics and structural results
	are compared with those obtained with standard single time-step methods,
	with and without SHAKE. The results demonstrate that, for peptides
	and proteins, the multiple time-step method yields stable trajectories
	with a saving of up to a factors of 4 in computer time. Some properties
	(e.g., relaxation times, hydrogen bonding characteristics) are given
	accurately in short simulations (10 ps) even from unstable integrators
	with large time steps. A series of longer simulations (100 ps) of
	BPTI confirm many of the results found in the shorter simulations.
	However, some larger differences in behavior result from the use
	of less stable integration algorithms; in one case, the simulation
	diverges. Also, use of the SHAKE algorithm for a hydrogen atoms containing
	bonds with a stable integrator is shown to affect some properties
	of the system (e.g., the spectral densities associated with the main
	chain and side chain torsional motions). The sensitivity appears
	to arise from the large number of hydrogen atoms in proteins and
	from the densely packed nature of the structures. Thus, a detailed
	treatment of the hydrogen atoms, including their bond length fluctuations,
	appears to be important for obtaining highly accurate dynamics of
	proteins.}
}

@ARTICLE{WATA95,
  author = {Masakatsu Watanabe and Martin Karplus},
  title = {Simulation of Macromolecules by Multiple-Time-Step Methods},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {5680--5697},
  number = {15}
}

@ARTICLE{WERN95a,
  author = {M. H. Werner and M. E. Bianchi and A. M. Gronenborn and G. M. Clore},
  title = {{NMR} spectroscopic analysis of the {DNA} conformation induced by
	the human testis determining factor {SRY}},
  journal = BCH,
  year = {1995},
  volume = {34},
  pages = {11998--12004},
  number = {37}
}

@ARTICLE{WERN95,
  author = {M. H. Werner and J. R. Huth and A. M. Gronenborn and G. M. Clore},
  title = {Molecular Basis of Human {46X,Y} Sex Reversal Revealed from the Three-Dimensional
	Solution Structure of the Human {SRY--DNA} Complex},
  journal = {Cell},
  year = {1995},
  volume = {81},
  pages = {705--714}
}

@ARTICLE{WEST95,
  author = {T.P. Westcott and I. Tobias and W.K. Olson},
  title = {Elasticity Theory and Numerical Analysis of {DNA} supercoiling: An
	application to {DNA} Looping},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {17926--17935}
}

@ARTICLE{WILB95,
  author = {Sigurd M. Wilbanks and David B. McKay},
  title = {How Potassium Affects the Activity of the Molecular Chaperone {H}sc70},
  journal = JBC,
  year = {1995},
  volume = {270},
  pages = {2251--2257}
}

@BOOK{WILT95,
  title = {Magnetic orientation in animals},
  publisher = {Springer},
  year = {1995},
  author = {Roswitha Wiltschko and Wolfgang Wiltschko},
  address = {Berlin}
}

@ARTICLE{WILT95A,
  author = {W. Wiltschko and R Wiltschko},
  title = {Migratory orientation of European robins is affected by the wavelength
	of light as well as by a magnetic pulse},
  journal = {J.~Comp.~Physiol.},
  year = {1995},
  volume = {177},
  pages = {363--369}
}

@INPROCEEDINGS{Wind95,
  author = {A. Windemuth},
  title = {Advanced Algorithms for Molecular Dynamics Simulation: The Program
	{PMD}},
  booktitle = {Parallel Computing in Computational Chemistry},
  year = {1995},
  editor = {Timothy G. Mattson},
  address = {Washington, D.C.},
  publisher = {ACS Books},
  note = {In press}
}

@ARTICLE{WOLF95,
  author = {S. A. Wolfe and A. E. Ferentz and V. Grantcharova and M. E. A. Churchill
	and G. L. Verdine},
  title = {Modifying the helical structure of {DNA} by design: recruitment of
	an architecture-specific protein to an enforced {DNA} bend},
  journal = {Chemistry and {B}iology},
  year = {1995},
  volume = {2},
  pages = {213--221},
  number = {4}
}

@BOOK{WOLF95A,
  title = {{Chromatin: Structure and Function}},
  publisher = {Academic Press},
  year = {1995},
  author = {A. Wolffe},
  address = {New York}
}

@BOOK{WOLK95,
  title = {Light Detectors, Photoreceptors, and Imaging Systems in Nature},
  publisher = {Oxford University Press},
  year = {1995},
  author = {J. Wolken},
  address = {New York}
}

@INPROCEEDINGS{WOOD95,
  author = {N. W. Woodbury and J. P. Allen},
  title = {The Pathway, Kinetics and Thrmodynamics of Electron Transfer in Wild
	Type and Mutant Reaction Centers of Purple Nonsulfur Bacteria},
  booktitle = {Anoxygenic Photosynthetic Bacteria},
  year = {1995},
  editor = {R.E. Blankenship and M.T. Madigan and C.E. Bauer},
  pages = {527--557},
  address = {Dordrecht},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{XU95B,
  author = {Dong Xu and Klaus Schulten},
  title = {Velocity Reassignment Echoes in Proteins},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {3124--3139},
  annote = {[Beckman Institute Technical Report TB-95-01]}
}

@ARTICLE{XSBK95,
  author = {Dong Xu and Klaus Schulten and Oren M. Becker and Martin Karplus},
  title = {Temperature Quench Echoes in Proteins},
  journal = {J. Chem.\ Phys.},
  year = {1995},
  volume = {103},
  pages = {3112--3123},
  annote = {[Beckman Institute Technical Report TB-95-02]}
}

@ARTICLE{XU95A,
  author = {Dong Xu and Klaus Schulten and Oren M. Becker and Martin Karplus},
  title = {Temperature Quench Echoes in Proteins},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {3112--3123},
  annote = {[Beckman Institute Technical Report TB-95-02]}
}

@ARTICLE{XU95C,
  author = {Dong Xu and Mordechai Sheves and Klaus Schulten},
  title = {Molecular Dynamics Study of the {M412} Intermediate of Bacteriorhodopsin},
  journal = BJ,
  year = {1995},
  volume = {69},
  pages = {2745--2760},
  number = {6}
}

@ARTICLE{Xu95,
  author = {G. H. Xu},
  title = {A New Parallel {N}-Body Gravity Solver---{TPM}},
  journal = { ASTROPHYSICAL-JOURNAL-SUPPLEMENT-SERIES},
  year = {1995},
  volume = {98},
  pages = {355--366},
  number = {1}
}

@ARTICLE{YANG95,
  author = {Y. Yang and T. P. Westcott and S. C. Pedersen and I. Tobias and W.
	K. Olson},
  title = {Effects of localized bending on {DNA} supercoiling},
  journal = TIBS,
  year = {1995},
  volume = {20},
  pages = {313--319},
  number = {8}
}

@ARTICLE{YYLD95,
  author = {Darrin M. York and Weitao T. Yang and Hsing Lee and Tom A. Darden
	and Lee G. Pedersen},
  title = {Toward the Accurate Modeling of {DNA}---the Importance of Long-Range
	Electrostatics},
  journal = {J. Amer.\ Chem.\ Soc.},
  year = {1995},
  volume = {117},
  pages = {5001--5002},
  number = {17}
}

@ARTICLE{YORK96,
  author = {D.~M..~York and W.~T.~Yang and H.~Lee and T.~Darden and others!!!},
  title = {Toward the accurate modeling of {DNA} - The importance of long-range
	electrostatics.},
  journal = JACS,
  year = {1995},
  volume = {117},
  pages = {5001--5002}
}

@ARTICLE{YOUN95a,
  author = {M.~A.~Young and G.~Ravishankar and D.~L.~Beveridge and H.~M.~Berman},
  title = {Analysis of local helix bending in crystal structures of {DNA} oligonucleotides
	and {DNA}-binding protein complexes.},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {2454--2468},
  annote = {catalog of base sequence dependent bending of {DNA}for A-type b-type
	drug and protein-bound DNA. uses MDtoolchest bending dials}
}

@ARTICLE{YOUN95,
  author = {Ralph G. Yount and David Lawson and Ivan Rayment},
  title = {Is Myosin a ``Back Door'' Enzyme?},
  journal = BJ,
  year = {1995},
  volume = {68},
  pages = {44s-49s}
}

@INPROCEEDINGS{ZELL95,
  author = {Michael Zeller and K. R. Wallace and Klaus Schulten},
  title = {Biological Visuo-Motor Control of a Pneumatic Robot Arm},
  booktitle = {Intelligent Engineering Systems Through Artificial Neural Networks},
  year = {1995},
  editor = {Dagli and others},
  volume = {5},
  pages = {645--650},
  address = {New York},
  publisher = {American Society of Mechanical Engineers},
  annote = {These are conference proceedings of ANNIE95; original "editor" field
	read: {Dagli and Akay and Chen and Fernandez and Ghosh}}
}

@INPROCEEDINGS{ZERN95,
  author = {M. C. Zerner},
  title = {A Quantum Chemical View of the Initial Photochemical Event in Photosynthesis},
  booktitle = {Proceedings of the Ecole de Physique des Houches},
  year = {1995},
  editor = {D. Bicout and M. J. Field},
  pages = {61--84},
  address = {Paris},
  publisher = {Les Editions de Physique, Springer}
}

@ARTICLE{ZhSc95,
  author = {Guihua Zhang and Tamar Schlick},
  title = {Implicit Discretization Schemes for {L}angevin Dynamics},
  journal = {Mol.\ Phys.},
  year = {1995},
  volume = {84},
  pages = {1077--1098}
}

@ARTICLE{ZhSk95,
  author = {M.~Q. Zhang and R.~D. Skeel},
  title = {Symplectic Integrators and the Conservation of Angular Momentum},
  journal = {J. Comput. Chem. },
  year = {1995},
  volume = {16},
  pages = { 365--369},
  nack = {NIH, DOE/NSF93, GC},
  nremark = {542.805 JO}
}

@MANUAL{ZHAO95,
  title = {Forms Library for X},
  author = {T. C. Zhao and M. Overmars},
  year = {1995},
  key = {XFORMS}
}

@ARTICLE{ZHOU95,
  author = {Feng Zhou and Klaus Schulten},
  title = {Molecular Dynamics Study of a Membrane--Water Interface},
  journal = JPC,
  year = {1995},
  volume = {99},
  pages = {2194--2208},
  techrep = {TB-94-11}
}

@ARTICLE{ZhBe95,
  author = {Ruhong Zhou and Bruce J. Berne},
  title = {A New Molecular Dynamics Method Combining the Reference System Propagator
	Algorithm with a Fast Multipole Method for Simulating Proteins and
	Other Complex Systems},
  journal = {J. Chem.\ Phys.},
  year = {1995},
  volume = {103},
  pages = {9444--9459},
  number = {21}
}

@ARTICLE{ZHOU95B,
  author = {R.~Zhou and B.~J.~Berne},
  title = {A new molecular dynamics method combining the reference system propagator
	algorithm with a fast multipole method for simulating proteins and
	other complex systems},
  journal = JCP,
  year = {1995},
  volume = {103},
  pages = {9444--9459},
  number = {21}
}

@ARTICLE{ZILL95A,
  author = {J.~Zilliacus and A.~P.~H.~Wright and J.~Carlstedt-Duke and J.~Gustafsson},
  title = {Structural determinants of {DNA}--binding specificity by steroid
	receptors.},
  journal = {MOLEND},
  year = {1995},
  volume = {9},
  pages = {389--400},
  annote = {minireview}
}

@ARTICLE{ZILL95,
  author = {J.~Zilliacus and A.~P.~H.~Wright and J.~Carlstedt-Duke and L.~Nilsson
	and J.~Gustafsson},
  title = {Modulation of {DNA}--binding specificity within the nuclear receptor
	family by substitutions at a single amino acid position.},
  journal = PSFG,
  year = {1995},
  volume = {21},
  pages = {57--67}
}

@INPROCEEDINGS{ZUBE95,
  author = {H. Zuber and R.J. Cogdell},
  title = {Structure and Organization of Purple Bacterial Antenna Complexes},
  booktitle = {Anoxygenic Photosynthetic Bacteria},
  year = {1995},
  editor = {R.E. Blankenship and M.T. Madigan and C.E. Bauer},
  pages = {315--348},
  address = {Dordrecht},
  publisher = {Kluwer Academic Publishers}
}

@TECHREPORT{sandia:decomp,
  author = {S. Plimpton and B. Hendrickson},
  title = {A New Parallel Method for Molecular Dynamics Simulation of Macromolecular
	Systems},
  institution = {Sandia National Laboratories},
  year = {1994},
  type = {Technical Report},
  number = {SAND94-1862},
  month = AUG
}

@MISC{DrDr94,
  author = {Cristina Draghicescu and Mircea Draghicescu},
  title = {A New Fast Summation Algorithm for the {N}-Body Problem},
  month = {July 22},
  year = {1994},
  note = {Overhead transparencies},
  nremark = {cris@math.uh.edu mircea@math.uh.edu}
}

@UNPUBLISHED{RoWe94,
  author = {Barry Robson and Paul Weiner et al},
  title = {Reduced variable MD},
  month = JUN,
  year = {1994},
  nremark = {That is another way to do long timestep MD}
}

@PHDTHESIS{BARS94A,
  author = {Daniel Barsky},
  title = {Diffusional Effects in Magnetic Resonance Imaging and Microscopy},
  school = {University of Illinois},
  year = {1994},
  address = {Urbana},
  month = MAY
}

@INPROCEEDINGS{crpc:space,
  author = {T. Clark and R. Hanxleden and J. McCammon and L. Scott},
  title = {Parallelizing Molecular Dynamics using Spatial Decomposition},
  booktitle = {Proceedings of the Scalable High Performance Computing Conference},
  year = {1994},
  address = {Knoxville, TN},
  month = MAY
}

@TECHREPORT{PVM94,
  author = {A. Geist and A. Beguelin and J. Dongarra and W. Jiang and R. Manchek
	and V. Sunderam},
  title = {{PVM}~3 Users Guide and Reference Manual},
  institution = {Oak Ridge National Laboratory},
  year = {1994},
  type = {Technical Manual},
  number = {ORNL/TM-12187},
  month = MAY
}

@ARTICLE{Lang94,
  author = {h p langtangen},
  title = {Numerical solution of first passage problems in random vibrations},
  journal = SJSC,
  year = {1994},
  volume = {15},
  pages = {977--996},
  area = {stoch dif eq}
}

@ARTICLE{VANG94,
  author = {R. {van Grondelle} and J. Dekker and T. Gillbro and V. Sundstrom},
  title = {Energy transfer and trapping in photosynthesis},
  journal = {Biochim. Biophys. Acta},
  year = {1994},
  volume = {1187},
  pages = {1--65}
}

@ARTICLE{ALLW94,
  author = {J. Abrahams and A. Leslie and R. Lutter and J. Walker},
  title = {Structure at 2.8~\AA\ resolution of {F$_1$-ATPase} from bovine heart
	mitochondria},
  journal = NAT,
  year = {1994},
  volume = {370},
  pages = {621--628}
}

@ARTICLE{AAEB94,
  author = {P. D. Adams and I. T. Arkin and D. M. Engelman and A. T. Br{\"u}nger},
  title = {Computational Searching and Mutagenesis Suggest a Structure for Phospholamban,
	a Cardiac Ion Channel},
  journal = SCI,
  year = {1994}
}

@ARTICLE{AdRe94,
  author = {S. B. Adams and E. Reisler},
  title = {Sequence 18--29 on Actin: Antibody and Spectroscopic Probing of Conformational
	Changes},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {14426--14433}
}

@BOOK{ALBE94,
  title = {The Cell},
  publisher = {Garland Publishing, Inc.},
  year = {1994},
  author = {B. Alberts and D. Bray and J. Lewis and M. Raff and K. Roberts and
	J. D. Watson},
  address = {New York \& London},
  edition = {3rd}
}

@ARTICLE{ALEX94,
  author = {U. Alexiev and T. Marti and M. P. Heyn and H. G. Khorana and P. Scherrer},
  title = {Covalently bound pH-indicator dyes at selected extracellular or cytoplasmic
	sites in bacteriorhodopsin. 2. Rotational orientation of helices
	{D} and {E} and kinetic correlation between {M} formation and proton
	release in bacteriorhodopsin micelles.},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {13693--13699}
}

@ARTICLE{ALLE94,
  author = {Bruce G. Allen and Michael P. Walsh},
  title = {The Biochemical Basis of the Regulation of Smooth-Muscle Contraction},
  journal = TIBS,
  year = {1994},
  volume = {19},
  pages = {362--368}
}

@ARTICLE{ALTE94,
  author = {Christian Altenbach and Duncan A. Greenhalgh and H. Gobind Khorana
	and Wayne L. Hubbell},
  title = {A collision gradient method to determine the immersion depth of nitroxides
	in lipid bilayers: application to spin-labeled mutatnts of bacteriorhodopsin},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {1667--1671}
}

@BOOK{ArFH94,
  title = {An Exploration of Chaos},
  publisher = {Elsevier Science},
  year = {1994},
  author = {J. Argyris and G. Faust and M. Haase},
  series = {Texts on Computational Mechanics Volume VII},
  address = {P. O. Box 945, Madison Square Station, New York, NY 10159--0945}
}

@ARTICLE{BABC94A,
  author = {M.~S.~Babcock and W.~K.~Olson},
  title = {The effect of mathematics and coordinate system on comparability
	and ''dependencies`` of nucleic acid structure parameters},
  journal = JMB,
  year = {1994},
  volume = {237},
  pages = {98--124}
}

@ARTICLE{BABC94,
  author = {Marla S. Babcock and Edwin P. D. Pednault and Wilma K. Olson},
  title = {Nucleic Acid Structure Analysis},
  journal = JMB,
  year = {1994},
  volume = {237},
  pages = {125--156}
}

@BOOK{BaNa94,
  title = {Scientific and Engineering {C\texttt{++}}: an introduction with advanced
	techniques and examples},
  publisher = {Addison-Wesley},
  year = {1994},
  author = {John J.\ Barton and Lee R.\ Nackman},
  address = {Reading, Massachusetts}
}

@INPROCEEDINGS{BEAS94,
  author = {R.C. Beason and P. Semm},
  title = {Detection of and receptors for magnetic fields in birds},
  booktitle = {Biological effects of electric and magnetic fields, vol I: Sources
	and mechanisms},
  year = {1994},
  editor = {D.C. Carpenter and S. Ayapetyan},
  pages = {241--260},
  address = {New York},
  publisher = {Acad.~Press}
}

@ARTICLE{BeLo94,
  author = {D. M. Beazley and P. S. Lomdahl},
  title = {Message-Passing Multi-Cell Molecular Dynamics on the {Connection
	Machine} 5},
  journal = {Parallel Computing},
  year = {1994},
  volume = {20},
  pages = {173--195}
}

@ARTICLE{BeGi94,
  author = {G. Benettin and A. Giorgilli},
  title = {On the {H}amiltonian Interpolation of Near to the Identity Symplectic
	Mappings with Application to Symplectic Integration Algorithms},
  journal = {J. Statist.\ Phys.},
  year = {1994},
  volume = {74},
  pages = {1117--1143},
  nremark = {[Also, tech.\ report DYS10-26, Univ. Milan., 1993]}
}

@ARTICLE{BEPP94,
  author = {Y. Beppu and T. Kakitani},
  title = {Theoretical Study of Color Control Mechanism in Retinal Proteins},
  journal = PCPB,
  year = {1994},
  volume = {59},
  pages = {660--669}
}

@ARTICLE{BEVE94,
  author = {D.~L.~Beveridge and G.~Ravishanker},
  title = {Molecular dynamics studies of {DNA}},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {246--255},
  annote = {review of simulations of {DNA}makes refs to all important papers
	and issures, but of course mostly sites himself, also in this issue
	of COSB are many other significant articles}
}

@MANUAL{MDMAN94,
  title = {How to Use Program {MD}},
  author = {Theoretical Biophysics},
  address = {Beckman Institute, 405~N.~Mathews Ave., Urbana, IL~61801, U.S.A.},
  year = {1994},
  institution = {University of Illinois at Urbana--Champaign}
}

@INCOLLECTION{BISH94,
  author = {Thomas C. Bishop and Klaus Schulten},
  title = {Molecular Dynamics Study of a Sequence Specific Protein--{DNA} Interaction},
  booktitle = {Computational Approaches in Supramolecular Chemistry},
  publisher = {Kluwer Academic Publishers},
  year = {1994},
  editor = {G. Wipff},
  pages = {419--439},
  address = {Boston},
  annote = {Submitted, Oct. 28 1993. The series will be NATO ASI series, need
	to find out which series and which volume. This is the proceedings
	of a conference of the same name.},
  tbtechrep = {TB-93-10}
}

@ARTICLE{BLOC94,
  author = {Steven Block and Karl Svoboda},
  title = {Biological Applications of Optical Forces},
  journal = ARBBS,
  year = {1994},
  volume = {23},
  pages = {247--285}
}

@TECHREPORT{BHER94,
  author = {J. Board and Z. Hakura and W. Elliot and W. Rankin},
  title = {Scalable Variants of Multipole-Accelerated Algorithms for Molecular
	Dynamics Applications},
  institution = {Duke University, Dept.\ of Elec.\ Engr.},
  year = {1994},
  number = {TR94-006}
}

@TECHREPORT{duke:fma,
  author = {J. Board and Z. Hakura and W. Elliot and W. Rankin},
  title = {Scalable Variants of Multipole-Accelerated Algorithms for Molecular
	Dynamics Applications},
  institution = {Duke University, Dept. of Elec. Engr.},
  year = {1994},
  type = {Technical Report},
  number = {TR94-006}
}

@ARTICLE{BOAR94,
  author = {Board, Jr., John A. and Laxmikant V. Kal{\'e} and Klaus Schulten
	and R.~D. Skeel and Tamar Schlick},
  title = {Modeling Biomolecules: Larger Scales, Longer Durations},
  journal = IEEECSE,
  year = {1994},
  volume = {{W}inter},
  pages = {19--30}
}

@ARTICLE{BoSc94,
  author = {P. B. Bochev and C. Scovel},
  title = {On quadratic invariants and symplectic structure},
  journal = {BIT},
  year = {1994},
  volume = {34},
  pages = {337--345},
  number = {3}
}

@ARTICLE{BONN94,
  author = {E. Bonnefoy and M. Takahashi and J. R. Yaniv},
  title = {{DNA-binding} parameters of the {HU} protein of {{\em Escherichia
	coli}}~to cruciform {DNA}},
  journal = JMB,
  year = {1994},
  volume = {242},
  pages = {116--129}
}

@ARTICLE{BOON94,
  author = {A.F. Boonstra and L. Germeroth and E.J. Boekema},
  title = {Structure of the Light Harvesting Antenna from {{\em {R}hodospirillum
	molischianum}} Studied by Electron Microscopy.},
  journal = {Biochim. et Biophys. Acta},
  year = {1994},
  volume = {1184},
  pages = {227--234}
}

@ARTICLE{BORK94,
  author = {P. Bork and L. Holm and C. Sander},
  title = {The immunoglobulin fold: structural classification, sequence patterns
	and common core},
  journal = JMB,
  year = {1994},
  volume = {242},
  pages = {309--320}
}

@ARTICLE{BrGR94,
  author = {A. Brandt and M. Galun and D. Ron},
  title = {Optimal multigrid algorithms for calculating thermodynamic limits},
  journal = {J. Stat. Phys.},
  year = {1994},
  volume = {74},
  pages = {313--348}
}

@ARTICLE{BRAN94,
  author = {U. Brandt and B. L. Trumpower},
  title = {The Protonmotive {Q} cycle in Mitochondria and Bacteria},
  journal = {CRC Crit.\ Rev.\ Biochem.},
  year = {1994},
  volume = {29},
  pages = {165--197}
}

@ARTICLE{BREM94,
  author = {A. Bremer and C. Henn and K. N. Goldie and A. Engel and P. R. Smith
	and U. Aebi},
  title = {Towards Atomic interpretation of {F}-actin filament three-dimensional
	reconstructions},
  journal = JMB,
  year = {1994},
  volume = {742},
  pages = {683--700}
}

@ARTICLE{BCOY94,
  author = {D. Brown and J. H. R. Clarke and M. Okuda and T. Yamazaki},
  title = {A domain decomposition parallel processing algorithm for molecular
	dynamics simulations of polymers},
  journal = {Comput. Phys. Commun.},
  year = {1994},
  volume = {83},
  pages = {1--13}
}

@ARTICLE{BROW94,
  author = {L. S. Brown and Y. Gat and M. Sheves and Y. Yamazaki and A. Maeda
	and R. Needleman and J. K. Lanyi},
  title = {THE RETINAL SCHIFF BASE-COUNTERION COMPLEX OF BACTERIORHODOPSIN -
	CHANGED GEOMETRY DURING THE PHOTOCYCLE IS A CAUSE OF PROTON TRANSFER
	TO ASPARTATE 85},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {12001--12011}
}

@ARTICLE{BrKi94,
  author = {Douglas Brune and Sangtae Kim},
  title = {Hydrodynamic Steering Effects in Protein Association},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1994},
  volume = {91},
  pages = {2930--2934}
}

@ARTICLE{BuPl94,
  author = {K. Burrage and E. Platen},
  title = {{R}unge-{K}utta methods for stochastic differential equations},
  journal = {Annals of Numerical Mathematics},
  year = {1994},
  volume = {1},
  pages = {63--78},
  number = {1-4},
  issn = {1021 2655}
}

@ARTICLE{LAND94,
  author = {C. C. ~Landel, P. J. Kushner, G. L. ~Greene},
  title = {The interaction of Human Estrogen Receptor with {DNA} is Modulated
	by Receptor--Associated Proteins.},
  journal = {Molecular Endocrinology},
  year = {1994},
  volume = {8},
  pages = {1407--1419}
}

@ARTICLE{CALH94,
  author = {M.W. Calhoun and J.W. Thomas and R.B. Gennis},
  title = {The cytochrome oxidase superfamily of redox-driven proton pumps},
  journal = TIBS,
  year = {1994},
  volume = {19},
  pages = {325}
}

@INPROCEEDINGS{CaMS94,
  author = {M.P. Calvo and A. Murua and J.M. Sanz-Serna},
  title = {Modified Equations for {ODE}s},
  booktitle = {Chaotic Numerics},
  year = {1994},
  editor = {Peter E. Kloeden and Kenneth J. Palmer},
  volume = {172},
  series = {Contemporary Mathematics},
  pages = {63--74},
  address = {Rhode Island},
  publisher = AMS
}

@ARTICLE{CANF94,
  author = {Jeff M. Canfield and R. Linn Belford and Peter G. Debrunner and Klaus
	Schulten},
  title = {A Perturbation Theory Treatment of Oscillating Magnetic Fields in
	the Radical Pair Mechanism},
  journal = CP,
  year = {1994},
  volume = {182},
  pages = {1--18},
  annote = {April 15 issue},
  tbtechrep = {TB-93-13}
}

@ARTICLE{DECA94,
  author = {C. De Caro and R. W. Visschers and R. van Grondelle and S. V{\"o}lker},
  title = {Inter- and Intraband Energy Transfer in LH2-Antenna Complexes of
	Purple bacteria. A Fluorescence Line-Narrowing and Hole-Burning Study},
  journal = JPC,
  year = {1994},
  volume = {98},
  pages = {10584--10590}
}

@ARTICLE{CASE94,
  author = {D. A. Case},
  title = {Normal mode analysis of protein dynamics},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {285--290}
}

@ARTICLE{CHIR94,
  author = {G. Chirico and J. Langowski},
  title = {Kinetics of {DNA} supercoiling studied by brownian dynamics simulation},
  journal = BP,
  year = {1994},
  volume = {34},
  pages = {415--433}
}

@ARTICLE{CHOW94,
  author = {C. S. Chow and J. P. Whitehead and S. J. Lippard},
  title = {{HMG} domain proteins induce sharp bends in cisplatin-modified {DNA}},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {15124--15130},
  number = {50}
}

@ARTICLE{CHRI94,
  author = {M.J. Chrispeels and P. Agre},
  title = {Aquaporins - Water Channel Proteins of Plant and Animal Cells},
  journal = {Trends in Biochemical Sciences},
  year = {1994},
  volume = {19},
  pages = {421}
}

@ARTICLE{CBSB94,
  author = {M. E. Clamp and P. G. Baker and C. J. Stirling and A. Brass},
  title = {Hybrid {M}onte {C}arlo: An Efficient Algorithm for Condensed Matter
	Simulation},
  journal = JCC,
  year = {1994},
  volume = {15},
  pages = {838--846},
  number = {8}
}

@INPROCEEDINGS{CHCS94,
  author = {T.~W. Clark and R.~van Hanxleden and J.~A. McCammon and L.~R. Scott},
  title = {Parallelizing Molecular Dynamics Using Spatial Decomposition},
  booktitle = {Proceedings of the Scalable High-Performance Computing Conference},
  year = {1994},
  pages = {95--102},
  address = {Los Alamitos, California},
  publisher = {IEEE Computer Society Press},
  nremark = {005.3SCA42P1994, http://sina.tcamc.uh.edu/~tclark/euler.ps}
}

@INPROCEEDINGS{CHMS94,
  author = {Terry W. Clark and Reinhard v.\ Hanxleden and J. Andrew McCammon
	and L. Ridgway Scott},
  title = {Parallelizing Molecular Dynamics Using Spatial Decomposition},
  booktitle = {Proceedings of the Scalable High-Performance Computing Conference},
  year = {1994},
  pages = {95--102},
  address = {Los Alamitos, California},
  publisher = {IEEE Computer Society Press},
  nremark = {005.3SCA42P1994, http://sina.tcamc.uh.edu/~tclark/euler.ps}
}

@ARTICLE{COLE94,
  author = {David E. Coleman and Albert M. Berghuis and Ethan Lee and Maurine
	E. Linder and Alfred G. Gilman and Stephen R. Sprang},
  title = {Structures of active conformations of {G$_{i\alpha1}$} and the mechanism
	of {GTP} hydrolysis},
  journal = SCI,
  year = {1994},
  volume = {265},
  pages = {1405--1412}
}

@ARTICLE{CoSW94,
  author = {Thomas Coleman and David Shalloway and Zhijun Wu},
  title = {A Parallel Build-Up Algorithm for Global Energy Minimizations of
	Molecular Clusters Using Effective Energy Simulated Annealing},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {171--185},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{COLM94,
  author = {P.M. Colman},
  title = {Structure-Based Drug Design},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {868--874}
}

@ARTICLE{Colt94,
  author = {David Colton},
  title = {Book Reviews, Inverse Problems in the Mathematical Sciences (Charles
	W. Groetsch)},
  journal = {SIAM Review},
  year = {1994},
  volume = {36},
  pages = {123--124},
  number = {1}
}

@INPROCEEDINGS{Corl94,
  author = {Robert M. Corless},
  title = {Error Backward},
  booktitle = {Chaotic Numerics},
  year = {1994},
  editor = {Peter E. Kloeden and Kenneth J. Palmer},
  volume = {172},
  series = {Contemporary Mathematics},
  pages = {31--62},
  address = {Rhode Island},
  publisher = AMS
}

@ARTICLE{CRIE94,
  author = {W. Crielaard and R.W. Visschers and G.J. Fowler and R. van Grondelle
	and K.J. Hellingwerf and C.N. Hunter},
  title = {Probing the {B}800 Bacteriochlorophyll Binding Site of the Accessory
	Light-Harvesting Complex from {{\em {R}hodobacter sphaeroides}} Using
	Site-Directed Mutants. {I}. {M}utagenesis, Effects on Binding, Function
	and Electrochromic Behaviour of its Carotenoids},
  journal = {Biochim. Biophys. Acta},
  year = {1994},
  volume = {1183},
  pages = {473}
}

@ARTICLE{CROS94,
  author = {R. H. Crosbie and C. Miller and P. Cheung and T. Goodnight and A.
	Muhlrad and E. Reisler},
  title = {Structural Connectivity in Actin: Effect of {C}-terminal modifications
	on the properties of actin},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {1957--1964}
}

@ARTICLE{CROT94,
  author = {D.~M.~Crothers},
  title = {Upsetting the Balance of Forces in {DNA}},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {1819--1820},
  annote = {bending of {DNA}by charges and intrinsics see STRA94 too}
}

@ARTICLE{CRUZ94,
  author = {L.~Cruzeiro-Hansson and J.~M.~Goodfellow},
  title = {Comparison of {DNA} Duplexes with and without O$^4$-Methylthymine:
	Nanosecond Molecular Dynamics Simulations},
  journal = JCS,
  year = {1994},
  volume = {90},
  pages = {1415--1427},
  number = {10},
  annote = {dodecanucleotide, 1ns, 4simulations,mismatched base-pairs, using
	amber v3a, all-atom, includes NA ions with 6waters each,shake, 2fs
	timestep, cut-off of 12A}
}

@ARTICLE{HaOG02,
  author = {Tomas Hansson and Chris Oostenbrink and Wilfred F van Gunsteren},
  title = {Molecular dynamics simulations},
  journal = {Current Opinion in Structural Biology},
  year = {2002},
  volume = {12},
  pages = {190--196}
}


@ARTICLE{DAGG94,
  author = {Valerie Dagget and Michael Levitt},
  title = {Protein Folding--Unfolding Dynamics},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {291--295}
}

@ARTICLE{DAVI94,
  author = {W. S. Davidson and D. L. Sparks and S. Lund-Katz and M. C. Phillips},
  title = {The Molecular Basis for the Difference in Charge Between Pre-$\beta$-
	and $\alpha$-Migrating High Density Lipoproteins},
  journal = JBC,
  year = {1994},
  volume = {269},
  pages = {8959--8965}
}

@ARTICLE{DLCR94,
  author = {Enrique M. {De La Cruz} and Thomas D. Pollard},
  title = {Transient Kinetic Analysis of Rhodamine Phalloidin Binding to Actin
	Filaments},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {14387--14392}
}

@ARTICLE{BUON94,
  author = {D. S. {Del\,Buono} and T. S. Cohen and P. J. Rossky},
  title = {Effects of Long-Range Interactions on the Dynamics of Ions in Aqueous
	Solution},
  journal = JML,
  year = {1994},
  volume = {60},
  pages = {221--236}
}

@ARTICLE{DeCR94,
  author = {G. S. Delbuono and T. S. Cohen and P. J. Rossky},
  title = {{E}ffects of long-range interactions on the dynamics of ions in aqueous-solution},
  journal = {J. Mol. Liq.},
  year = {1994},
  volume = {60},
  pages = {221}
}

@ARTICLE{DELL94,
  author = {M. J. Dellwo and D. M. Schneider and A. J. Wand},
  title = {Modifications of the Rate Matrix Required for Quantitative Analysis
	of {NOESY} Spectra of Proteins},
  journal = JMRB,
  year = {1994},
  volume = {103},
  pages = {1--9}
}

@ARTICLE{DERE94,
  author = {U. Derewenda and L. Swenson and Y. Wei},
  title = {Conformational Lability Of Lipases Observed In The Absence Of An
	Oil-Water Interface: Crystallographic Studies Of Enzymes From The
	Fungi Humicola Lanuginosa, And Rhizopus Delemar},
  journal = {Journal of lipid research},
  year = {1994},
  volume = {35},
  pages = {524--534}
}

@ARTICLE{Drag94,
  author = {C.I. Draghicescu},
  title = {An Efficient Implementation of Particle Methods for the Incompressible
	{E}uler Equations},
  journal = SJNA,
  year = {1994},
  volume = {31},
  pages = {1090--1108},
  number = {4}
}

@BOOK{DREN94,
  title = {Principles of Protein X-ray Crystallography},
  publisher = {Springer-Verlag},
  year = {1994},
  author = {J. Drenth},
  address = {New York}
}

@INCOLLECTION{Earn94,
  author = {David J. D. Earn},
  title = {Symplectic Integration Without Roundoff Error},
  booktitle = {Ergodic Concepts in Stellar Dynamics},
  publisher = {Springer-Verlag},
  year = {1994},
  editor = {V. G. Gurzadyan and D. Pfenniger},
  pages = {122--130},
  address = {Heidelberg},
  nremark = {also Weizmann Institute of Science, August 1993, preprint; Lecture
	Notes in Physics 430}
}

@ARTICLE{EGEL94,
  author = {Edward Egelman},
  title = {The ghost of ribbon's past},
  journal = CB,
  year = {1994},
  volume = {4},
  pages = {79--81}
}

@ARTICLE{ENGE94,
  author = {A. Engel and T. Walz and P. Agre},
  title = {The Aquaporin Family of Membrane Water Channels},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {545}
}

@ARTICLE{ERIC94,
  author = {Harold Erickson},
  title = {Reversible unfolding of fibronectin type {I}{I}{I} and immunoglobulin
	domains provides the structural basis for stretch and elasticity
	of titin and fibronectin},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {10114--10118}
}

@ARTICLE{ERIE94,
  author = {D.~A.~Erie and G.~Yang and H.~C.~Schultz and C.~Bustamante},
  title = {{DNA} bending by Cro protein in specific and nonspecific complexes:
	implications for protein site recognition and specificity.},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {1562--1566}
}

@INCOLLECTION{ERIK94,
  author = {M.~A.~L.~Eriksson and T.~H{\"a}rd and L.~Nilsson},
  title = {Molecular dynamics simulation of a {DNA} binding protein free and
	in complex with {DNA}},
  booktitle = {Computational Approaches in Supramolecular Chemistry},
  publisher = {Kluwer Academic Publishers},
  year = {1994},
  editor = {G. Wipff},
  pages = {457--475},
  address = {Boston},
  annote = {similar work to BISH94 and should site both simultaneously}
}

@ARTICLE{ERML94,
  author = {U. Ermler and G. Fritzsch and S.K. Buchanan and H. Michel},
  title = {Structure of the Photosynthetic Reaction Center from {{\em {R}hodobacter
	sphaeroides}} at 2.65 {{\AA}} Resolution: Cofactors and Protein-cofactor
	Interactions},
  journal = {Structure},
  year = {1994},
  volume = {2},
  pages = {925--936}
}

@INCOLLECTION{EVAN94,
  author = {E. Evans and R. Merkel and K. Ritchie and S. Tha and A. Zilker},
  title = {Picoforce method to probe submicroscopic actions in biomembrane adhesion},
  booktitle = {Studying Cell Adhesion},
  publisher = {Springer-Verlag},
  year = {1994},
  editor = {P. Bongrand and P. M. Claesson and A. S. G. Curtis},
  pages = {125--140},
  address = {Berlin},
  annote = {biomembrane force probe ref., another is EVAN95}
}

@ARTICLE{FALC94,
  author = {L. Falciola and A. I. H. Murchie and D. M. J. Lilley and M. E. Bianchi},
  title = {Mutational analysis of the {DNA} binding domain {A} of chromosomal
	protein {HMG1}},
  journal = NAR,
  year = {1994},
  volume = {22},
  pages = {285--292},
  number = {3}
}

@ARTICLE{FARS94,
  author = {R. Farshoosh and V. Chynwat and R. Gebhard and J. Lugtenburg and
	H.A. Frank},
  title = {Triplet energy transfer between bacteriochlorophyll and carotenoids
	in B850 light-harvesting complexes of {\em Rhodobacter sphaeroides}
	R-26.1},
  journal = {Photosyn.~Res.},
  year = {1994},
  volume = {42},
  pages = {157--166}
}

@ARTICLE{FAUR94,
  author = {P. Faure and A. Micu and D. Perahia and J. Doucet and J.C. Smith
	and J.P. Benoit},
  title = {Correlated intramolecular motions and diffuse {X}-ray scattering
	in lysozyme},
  journal = STRB,
  year = {1994},
  volume = {1},
  pages = {124--128}
}

@ARTICLE{FENG94,
  author = {J.~Feng and R.~C.~Johnson and R.~E.~Dickerson},
  title = {Hin recombinase bound to {DNA}: the origin of specificity in major
	and minor groove interactions.},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {348--355}
}

@ARTICLE{FENG94a,
  author = {Yan Feng and Donald R. Menick and Bernice M. Katz and Charles J.
	Beischel and E. Starr Hazard and Saurav Misra and Thomas G. Ebrey
	and Rosalie K. Crouch},
  title = {Probing of the Retinal Binding Site of Bacteriorhodopsin by Affinity
	Labeling},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {11624--11630}
}

@ARTICLE{FENL94,
  author = {Marcia O. Fenley and Wilma K. Olson and Irwin Tobias and Gerald S.
	Manning},
  title = {Electrostatic effects in short superhelical {DNA}},
  journal = BPC,
  year = {1994},
  volume = {50},
  pages = {255--271}
}

@ARTICLE{FMMGK94,
  author = {David M. Ferguson and Amanda Marsh and Thomas Metzger and David G.
	Garrett and Keith Kastella},
  title = {Conformational Searches for the Global Minimum of Protein Models},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {209--227},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{FERN94,
  author = {J. A. Fernandez and B. O. Villoutreix and T. M. Hackeng and J. H.
	Griffin and B. N. Bouma},
  title = {Analysis of protein {S C4b}-binding protein interactions by homology
	modeling and inhibitory antibodies},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {11073--11078}
}

@ARTICLE{Finc94,
  author = {D. Fincham},
  title = {Optimisation of the {E}wald sum for large systems},
  journal = {Mol. Sim.},
  year = {1994},
  volume = {13},
  pages = {1--9}
}

@ARTICLE{FLAH94,
  author = {Kevin M. Flaherty and Sigurd M. Wilbanks and Camille DeLuca-Flaherty
	and David B. McKay},
  title = {Structural Basis of the 70-Kilodalton Heat Shock Cognate Protein
	{ATP} Hydrolytic Activity},
  journal = JBC,
  year = {1994},
  volume = {269},
  pages = {12899--12907}
}

@ARTICLE{FLEM94,
  author = {G.R. Fleming and R. {van Grondelle}},
  title = {The Primary Steps of Photosynthesis},
  journal = {Physics Today},
  year = {1994},
  volume = {47},
  pages = {48--55}
}

@ARTICLE{FLOR94,
  author = {Ernst-Ludwig Florin and Vincent T. Moy and Hermann E. Gaub},
  title = {Adhesion Force Between Individual Ligand-Receptor Pairs},
  journal = SCI,
  year = {1994},
  volume = {264},
  pages = {415--417},
  annote = {june 1}
}

@ARTICLE{FlSZ94,
  author = {Flytzanis, N. and A.V. Savin and Y. Zolotaryuk},
  title = {Soliton dynamics in a thermalized molecular chain with transversal
	degree of freedom},
  journal = {PHYSICS LETTERS A},
  year = {1994},
  volume = {193},
  pages = {148},
  number = {2}
}

@BOOK{Flor69,
  author = {P. J. Flory},
  title = {Statistical Mechanics of Chain Molecules},
  publisher = {Interscience},
  year = {1969},
  address = {New York}
}


@ARTICLE{FoSm94,
  author = {T. Forester and W. Smith},
  title = {On Multiple Time-Step Algorithms and the {E}wald Sum},
  journal = {Mol.\ Sim.},
  year = {1994},
  volume = {13},
  pages = {195--204},
  number = {3},
  nabstract = {We show how standard multiple time-step algorithms devised for systems
	with short-range potentials can be used successfully in simulations
	of periodic systems with long-range (Coulombic) potentials. Three
	strategies for incorporating the Ewald sum into a multiple time-step
	algorithm are considered. These are (i) evaluation of reciprocal
	space terms every time-step (ii) evaluating reciprocal space terms
	once every n time-steps and placing these terms in with the slowly
	varying forces and energies (iii) a modified form of the second strategy
	in which primary shell (close) electrostatic interactions are evaluated
	directly and the more distant interactions handled by the Ewald sum
	(once every n time-steps). Only the first and third approaches give
	satisfactory thermodynamic results. The third strategy is much more
	efficient than the first. With the third strategy substantial savings
	in cpu time are achieved in both the real space and, most importantly,
	the reciprocal space terms of the Ewald sum. This is achieved without
	significant loss of accuracy or stability. Overall execution time
	is decreased by a factor of between 2 and 3.}
}

@ARTICLE{FoSu94,
  author = {B. M. Forrest and U. W. Suter},
  title = {Hybrid {M}onte {C}arlo Simulations of dense polymer systems},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {101},
  remark = {Condensed matter HMC}
}

@ARTICLE{FoSu94b,
  author = {B. M. Forrest and U. W. Suter},
  title = {Generalized coordinate hybrid {M}onte {C}arlo},
  journal = {Mole. Phy..},
  year = {1994},
  volume = {82},
  remark = {generazed coordinaterHMC}
}

@ARTICLE{FKLS94,
  author = {Forsten, K. E. and Kozack, R. E. and Lauffenburger, D. A. and Subramaniam,
	S.},
  title = {Numerical Solution of the Nonlinear {P}oisson--{B}oltzmann Equation
	for a Membrane--Electrolyte System},
  journal = {J. Phys.\ Chem.},
  year = {1994},
  volume = {98},
  pages = {5580}
}

@ARTICLE{FOWL94,
  author = {G.J.S. Fowler and G.D. Sockalingum and B. Robert and C.N. Hunter},
  title = {Blue Shifts in Bacteriochlorophyll Absorbance Correlate with Changed
	Hydrogen Bonding Patterns in Light-Harvesting 2 Mutants of {\em {R}hodobacter
	Sphaeroides} with Alterations at $\alpha$-{T}yr-44 and $\alpha$-{T}yr-45},
  journal = {Biochemical Journal},
  year = {1994},
  volume = {299},
  pages = {695}
}

@BOOK{FoWM94,
  title = {Parallel Computing Works!},
  publisher = {Morgan Kauffman},
  year = {1994},
  author = {G. C. Fox and R. D. Williams and P. C. Messina},
  address = {San Francisco},
  isbn = {1-55860-253-4}
}

@ARTICLE{GEOU94,
  author = {C. Geourjon and G. Deleage},
  title = {{SOPM}: a self optimised prediction method for protein secondary
	structure prediction.},
  journal = {Protein Engineering},
  year = {1994},
  volume = {7},
  pages = {157}
}

@ARTICLE{GERG94,
  author = {C. Gergely and C. Ganea and G. Varo},
  title = {Combined Optical and Photoelectric Study of the Photocycle of 13-{\it
	cis} Bacteriorhodopsin},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {855--861}
}

@ARTICLE{GERS94,
  author = {M. Gerstein and A. M. Lesk and C. Chothia},
  title = {Structural mechanisms for domain movements in proteins},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {6739--6749}
}

@ARTICLE{GILS94,
  author = {M. K. Gilson and T. P. Straatsma and J. A. McCammon and D. R. Ripoll
	and C. H. Faerman and P. H. Axelsen and I. Silman and J. L. Sussman},
  title = {Open "Back Door" in a molecular dynamics simulation of Acetylcholinesterase},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {1276--1278}
}

@ARTICLE{GOVI94,
  author = {R. Govindjee and S. Balashov and T. Ebrey},
  title = {Lowering the Intrinsic {pK$_a$} of the Chromophore's {Schiff} Base
	Can Restore Its Light-induced Deprotonation in the Inactive {Tyr-57}\,$\rightarrow$\,{Asn}
	Mutant of Bacteriorhodopsin},
  journal = JBC,
  year = {1994},
  volume = {269},
  pages = {14353--14354}
}

@ARTICLE{GRAN94,
  author = {R.~A.~Grant and C.~N.~Hiremath and D.~J.~Filman and R.~Syed and K.~Andries
	and J.~M.~Hogle},
  title = {Structures of poliovirus complexes with anti-viral drugs: implications
	for viral stability and drug design},
  journal = CB,
  year = {1994},
  volume = {4},
  pages = {784--797},
  number = {6}
}

@ARTICLE{Gree94,
  author = {L. Greengard},
  title = {Fast Algorithms For Classical Physics},
  journal = {Science},
  year = {1994},
  volume = {265},
  pages = {909--914}
}

@ARTICLE{GrDo94,
  author = {Niels Gronbech-Jensen and Sebastian Doniach},
  title = {Long-time overdamped {L}angevin dynamics of molecular chains},
  journal = {J. Comput.\ Chem.},
  year = {1994},
  volume = {15},
  pages = {997--1012},
  number = {9},
  nremark = {Brownian dynamics}
}

@BOOK{GrLS94,
  title = {Using {MPI} - Portable Parallel Programming with the Message-Passing
	Interface},
  publisher = {{MIT} Press},
  year = {1994},
  author = {W. Gropp and E. Lusk and A. Skjellum}
}

@BOOK{GRKH94,
  title = {Statistical Physics of Macromolecules},
  publisher = {AIP Press},
  year = {1994},
  author = {Alexander Yu.~Grosberg and Alexei R. Khokhlov},
  series = {AIP Series in Polymers and Complex Materials},
  address = {New York}
}

@ARTICLE{GROS94,
  author = {R. Grosschedl and K. Giese and J. Pagel},
  title = {{HMG} domain proteins: {A}rchitectural elements in the assembly of
	nucleoprotein structures},
  journal = {Trends in Genetics},
  year = {1994},
  volume = {10},
  pages = {94--100}
}

@PHDTHESIS{Grub94,
  author = {Helmut Grubm{\"u}ller},
  title = {Molekular dynamik von {P}roteinen auf langen {Z}eitskalen},
  school = {\mbox{Physik-Dept. der Tech. Univ. M\"unchen}},
  year = {1994},
  address = {Munich},
  nremark = {the chaos observed here is much greater than that observed by AlTi87
	apparently because of the exponential dependence on temperature}
}

@ARTICLE{GrTa94,
  author = {Helmut Grubm{\"u}ller and Paul Tavan},
  title = {Molecular Dynamics of Conformational Substates for a Simplified Protein
	Model},
  journal = {J. Chem.\ Phys.},
  year = {1994},
  volume = {101},
  pages = {5047--5057},
  number = {6}
}

@ARTICLE{GRON94,
  author = {N.\ Gr{\o}nbech-Jensen and S.\ Doniach},
  title = {Long-Time Overdamped Langevin Dynamics of Molecular Chains},
  journal = JCC,
  year = {1994},
  volume = {15},
  pages = {997--1012}
}

@ARTICLE{WANG94A,
  author = {Y. Guan and H. Zhang and R. N. H. Konings and C. W. Hilbers and T.
	C. Terwillinger and A. H.-J. Wang},
  title = {Crystal structures of {Y41H} and {Y41F} mutants of gene {V} protein
	from {Ff} phage suggest possible proyein-protein interacrions in
	the {GVP-ssDNA} complex},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {7768--7778}
}

@ARTICLE{GuSt94,
  author = {F. Guarnieri and W. C. Still},
  title = {A Rapidly Convergent Simulation Method---Mixed {M}onte {C}arlo Stochastic
	Dynamics},
  journal = JCC,
  year = {1994},
  volume = {15},
  pages = {1302--1310},
  number = {11},
  abstract = {Although {M}onte {C}arlo and molecular dynamics are the primary methods
	used for free energy simulations of molecular systems, their application
	to molecules that have multiple conformations separated by energy
	barriers of greater than or equal to 3 kcal/mol is problematic because
	of slow rates of convergence. In this article we introduce a hybrid
	simulation method termed MC-SD which mixes {M}onte {C}arlo (MC) and
	stochastic dynamics (SD). This new method generates a canonical ensemble
	via alternating MC and SD steps and combines the local exploration
	strengths of dynamics with the barrier-crossing ability of large-step
	{M}onte {C}arlo. Using calculations on double-well potentials and
	long simulations (10(8) steps of MC and 1 mu s of SD) of the simple,
	conformationally flexible molecule n-pentane, we find that MC-SD
	simulations converge faster than either MC or SD alone and generate
	ensembles which are equivalent to those created by classical MC or
	SD. Using pure SD at 300 K, the conformational populations of n-pentane
	are shown to be poorly converged even after a full microsecond of
	simulation.},
  annote = {mixed stochastic MD and MC - pointed out by Mark Lipton, Chemistry,
	Purdue}
}

@ARTICLE{GSAL94,
  author = {L. W. Guddat and L. Shanand and J. M. Anchin and D. S. Linthicum
	and A. B. Edmundson},
  title = {Local and transmitted conformational changes on complexation of an
	anti-sweetener Fab},
  journal = {J. Mol.\ Biol.},
  year = {1994},
  volume = {236},
  pages = {247--274},
  number = {1}
}

@ARTICLE{HACK94,
  author = {D.D. Hackney},
  title = {Evidence for alternating head catalysis by kinesin during microtubule-stimulated
	{ATP} hydrolysis},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {6865--6869}
}

@ARTICLE{Hair94,
  author = {E. Hairer},
  title = {Backward error analysis of numerical integrators and symplectic methods},
  journal = {Annals of Numer.\ Math.},
  year = {1994},
  volume = {1},
  pages = {107--132}
}

@ARTICLE{HANE94,
  author = {S. W. Haney},
  title = {Is {C\texttt{++}} Fast Enough For Scientific Computing?},
  journal = CIP,
  year = {1994},
  volume = {8},
  pages = {690--694},
  number = {6}
}

@ARTICLE{HANS94,
  author = {H.~G.~Hansma and K.~A.~},
  title = {Bending and Straightening of {DNA} Induced by the Same Ligand: Characterization
	with the Atomic Force Microscope},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {8436--8441},
  number = {28}
}

@ARTICLE{HaOk94,
  author = {U.H.E. Hansmann and Y. Okamoto},
  title = {Comparative study of multicanonical and simulated annealing Algorithms
	in the protein folding problem},
  journal = {PHYSICA A},
  year = {1994},
  volume = {212},
  pages = {415},
  number = {3 and 4},
  nremark = {MATHEMATICAL STATISTICAL PHYSICS}
}

@ARTICLE{HAQQ94,
  author = {C. M. Haqq and C-Y. King and E. Ukiyama and S. Falsafi and T. N.
	Haqq and P. K. Donahoe and M. A. Weiss},
  title = {Molecular basis of mammalian sexual determination: activation of
	{M}\"ullerian {I}nhibiting {S}ubstance gene expression by {SRY}},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {1494--1500}
}

@ARTICLE{HARK94,
  author = {T.T. Harkins and C.B. Grissom},
  title = {Magnetic field effects on {B}$_{12}$ Ethanolamine Ammonia Lyase:
	Evidence for a Radical Mechanism},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {958--960}
}

@ARTICLE{HARL94,
  author = {K. Harlos and D. M. A. Martin and D. P. O'Brien and E. Y. Jones and
	D. I. Stuart and I. Polikarpov and A. Miller and E. G. D. Tuddenham
	and C. W. G. Boys},
  title = {Crystal structure of the extracellular region of human tissue factor},
  journal = NAT,
  year = {1994},
  volume = {370},
  pages = {662--666}
}

@ARTICLE{HARR94,
  author = {Lester F.~Harris and Michael R.~Sullivan and Pamela D.~Popken-Harris
	and David F.~Hickok},
  title = {Molecular Dynamics Simulations in Solvent of the Glucocorticoid Receptor
	Protein in Complex with a Glucocorticoid Response Element {DNA} Sequence},
  journal = JBSD,
  year = {1994},
  volume = {12},
  pages = {249--270},
  number = {2},
  annote = {another MD simulation of GR-DBD/DNA complex with cut-off, they report
	a bending and a bp opening event for the DNA, as well as many additional
	contacts not in x-stal. simulation based on modeling not x-stal}
}

@ARTICLE{HaYa94,
  author = {A. Harten and I. Yad-Shalom},
  title = {Fast Multiresolution Algorithms for Matrix-Vector Multiplication},
  journal = SJNA,
  year = {1994},
  volume = {31},
  pages = {1443--1453}
}

@ARTICLE{HAUS94,
  author = {T. Hauss and G. Buldt and M. P. Heyn and N. A. Dencher},
  title = {LIGHT-INDUCED ISOMERIZATION CAUSES AN INCREASE IN THE CHROMOPHORE
	TILT IN THE {M} INTERMEDIATE OF BACTERIORHODOPSIN - A NEUTRON DIFFRACTION
	STUDY},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {11854--11858}
}

@ARTICLE{HEBE94,
  author = {J.~Heberle and J.~Riesle and G.~Thiedemann and D.~Oesterhelt and
	N.A.~Dencher},
  title = {Proton migration along the membrane surface and retarded surface
	to bulk transfert},
  journal = NAT,
  year = {1994},
  volume = {370},
  pages = {379--382}
}

@ARTICLE{HEGI94,
  author = {L.~Heginbotham and Z.~Lu and T.~Abramson and R.~Mac{K}innon.},
  title = {Mutations in the {K}$^+$ channel signature sequence},
  journal = BJ,
  year = {1994},
  volume = {64},
  pages = {1061--1067},
  annote = {this is about the selectivity filter}
}

@ARTICLE{VONH94a,
  author = {G. von Heijne},
  title = {Membrane proteins: from sequence to structure.},
  journal = {Annual Review of Biophysics and Biomolecular Structure },
  year = {1994},
  volume = {23},
  pages = {167}
}

@INCOLLECTION{HESK93b,
  author = {Tom Heskes},
  title = {Stochastics of On-Line Backpropagation},
  booktitle = {Proceedings of the European Symposium on Artificial Neural Networks},
  year = {1994},
  pages = {223--228},
  tbtechrep = {TB-93-11}
}

@TECHREPORT{HESK94,
  author = {Tom Heskes and Wim Wiegerinck and Andrzej Komoda},
  title = {Scaling Properties of On-line Learning with Momentum},
  institution = {University of Illinois},
  year = {1994},
  type = {Beckman Institute Technical Report},
  number = {TB-94-03},
  annote = {Submitted to International Conference on Neural Networks, Orlando,
	1994},
  tbtechrep = {TB-94-03}
}

@ARTICLE{HESS94a,
  author = {S. Hess and K. J. Visscher and T. Pullerits and V. Sundstrom and
	G. J. S. Fowler and C. N. Hunter},
  title = {Enhanced Rates of Subpicosecond Energy Transfer in Blue-shifted Light
	Harvesting LH2 Mutants of Rhodobacte r sphaeroides},
  journal = {Biochemistry},
  year = {1994},
  volume = {33},
  pages = {8300--8305}
}

@ARTICLE{HESS94,
  author = {Ted Hesselroth and Kakali Sarkar and P. Patrick van der Smagt and
	Klaus Schulten},
  title = {Neural Network Control of a Pneumatic Robot Arm},
  journal = IEEESMC,
  year = {1994},
  volume = {24},
  pages = {28--37},
  number = {1},
  tbtechrep = {TB-92-15}
}

@ARTICLE{HiGW94,
  author = {K. A. Hibbits and D. S. Gill and R. C. Willson},
  title = {Isothermal Titration Calorimetric Study of the Association of Hen-Egg
	Lysozyme and the Anti-Lysozyme Antibody {H}y{HEL}-5},
  journal = {Biochem.},
  year = {1994},
  volume = {33},
  pages = {3584}
}

@ARTICLE{HKSS94b,
  author = {M. Holst and R. Kozack and F. Saied and S. Subramaniam},
  title = {Treatment of electrostatic effects in proteins: {M}ultigrid-based
	{N}ewton iterative method for solution of the full nonlinear {Poisson--Boltzmann}
	equation},
  journal = {{P}roteins: {S}tructure, {F}unction, and {G}enetics},
  year = {1994},
  volume = {18},
  pages = {231--245},
  number = {3},
  remark = {[Beckman Institute Technical Report UIUC-BI-MB-93-01]}
}

@ARTICLE{HKSS94a,
  author = {M. Holst and R.~E.~Kozack and F.~Saied and S.~Subramaniam},
  title = {Protein Electrostatics: Rapid Multigrid-based {N}ewton Algorithm
	for Solution of the Full Nonlinear {P}oisson--{B}oltzmann Equation},
  journal = {J. Biomol.\ Struct.\ Dyn.},
  year = {1994},
  volume = {11},
  pages = {1437--1445},
  number = {6},
  nack = {presumably this is the paper submitted to Nature that acks DOE}
}

@BOOK{Hone94,
  title = {Stochastic Dynamical Systems: Concepts, Numerical Methods, Data Analysis},
  publisher = {VCH},
  year = {1994},
  author = {J. Honerkamp},
  place = {New York}
}

@TECHREPORT{HUMP94,
  author = {William Humphrey and Andrew Dalke},
  title = {{VMD} User Guide ({Version} 0.94)},
  institution = {University of Illinois},
  year = {1994},
  type = {Beckman Institute Technical Report},
  number = {TB-94-07},
  tbtechrep = {TB-94-07}
}

@MANUAL{HUMP94-LONG,
  title = {{VMD} User Guide ({Version} 0.94)},
  author = {William Humphrey and Andrew Dalke},
  address = {405~N.~Mathews Ave., Urbana, IL~61801, U.S.A.},
  year = {1994},
  note = {[Beckman Institute Technical Report TB-94-07].},
  institution = {Theoretical Biophysics Group at the University of Illinois at Urbana--Champaign,
	Beckman Institute},
  tbtechrep = {TB-94-07}
}

@ARTICLE{HUMP94A,
  author = {William Humphrey and Ilya Logunov and Klaus Schulten and Mordechai
	Sheves},
  title = {Molecular Dynamics Study of Bacteriorhodopsin and Artificial Pigments},
  journal = {Biochemistry},
  year = {1994},
  volume = {33},
  pages = {3668--3678},
  tbtechrep = {TB-93-09}
}

@ARTICLE{HuFB94,
  author = {Darryl D. Humphreys and Richard A. Friesner and Bruce J. Berne},
  title = {A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules},
  journal = JPC,
  year = {1994},
  volume = {98},
  pages = {6885--6892},
  number = {27},
  nabstract = {We present a computationally efficient molecular dynamics algorithm
	designed to take advantage of the inherent separation of time scales
	in biomolecular systems. The algorithm is essentially a generalization
	of the previously introduced reversible reference system propagation
	algorithm (r-RESPA) which employs a Trotter factorization of the
	Liouville propagator to generate numerical integration schemes for
	molecular dynamics applications. The method is compared with the
	velocity Verlet integration algorithm in a molecular dynamics (MD)
	simulation of the protein crambin in vacuo. The multiple-time-step
	algorithm is shown to be able to take a much larger time step for
	a comparable level of accuracy than that of the standard method,
	leading to a 4-5-fold reduction in the CPU time required to calculate
	the nonbonded forces.}
}

@ARTICLE{HUXL94,
  author = {Hugh E. Huxley and Alex Stewart and Hernando Sosa and Tom Irving},
  title = {{X}-ray diffraction Measurements of the Extensibility of Actin and
	Myosin Filaments in Contracting Muscle},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {2411--2421}
}

@ARTICLE{IHLE94,
  author = {W. D. Ihlenfeldt and Y. Takahashi and H. Abe},
  title = {Computation and Management of Chemical Properties in CACTVS: An Extensible
	Networked Approach Toward Modularity and Compatibility},
  journal = {J. Chem. Inf. Comput. Sci.},
  year = {1994},
  volume = {34},
  pages = {109}
}

@ARTICLE{Irba94,
  author = {A. Irb{\"a}ck},
  title = {Hybrid {M}onte {C}arlo simulation of polymer chains},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {101},
  pages = {1661--1667},
  number = {2},
  remark = {Condensed matter HMC}
}

@MISC{JAVA,
  author = {Java},
  title = {Java Technology},
  year = {1994},
  note = {\url{http://java.sun.com}}
}

@ARTICLE{JAYA94,
  author = {B.~Jayaram and N.~Aneja and E.~Rajasekaran and V.~Arora and A. Das
	and V.~Ranganathan and V.~Gupta},
  title = {Modelling {DNA} in aqueous solutions},
  journal = {J.\ Sci.\ Indust.\ Res.},
  year = {1994},
  volume = {53},
  pages = {88--105},
  annote = {review of modelling {DNA}in aqueous solutions}
}

@ARTICLE{JOAC94,
  author = {A.~Joachimiak and T.~E.~Haran and P.~B.~Sigler.},
  title = {Mutagenesis supports water mediated recognition in the {\em trp}
	repressor-operator system},
  journal = EMBO,
  year = {1994},
  volume = {13},
  pages = {367--372}
}

@INPROCEEDINGS{BHEG94,
  author = {John A. Board, Jr. and Ziyad S. Hakura and William D. Elliot and
	Daniel C. Gray and William J. Blanke and James F. Leathrum, Jr.},
  title = {Scalable Implementations of Multipole-Accelerated Algorithms for
	Molecular Dynamics},
  booktitle = {Proceedings of the Scalable High-Performance Computing Conference},
  year = {1994},
  pages = {87--94},
  address = {Los Alamitos, California},
  publisher = {IEEE Computer Society Press},
  nremark = {also, Duke University, Dept.\ of Elec.\ Engr., TR94-002}
}

@ARTICLE{JOHN94,
  author = {M. S. Johnson and N. Srinivasan and R. Sowdhamini and T. L. Blundell},
  title = {Knowledge-based protein modeling},
  journal = {Critical Reviews in Biochemistry and Molecular Biology},
  year = {1994},
  volume = {29},
  pages = {1--68},
  number = {1}
}

@ARTICLE{JONE94,
  author = {D. N. M. Jones and M. A. Searles and G. L. Shaw and M. E. A. Churchill
	and S. S. Ner and J. Keeler and A. A. Travers and D. Neuhaus},
  title = {The solution structure and dynamics of the {DNA}-binding domain of
	{HMG-D} from {{\em Drosophila melanogaster}}},
  journal = {Structure},
  year = {1994},
  volume = {2},
  pages = {609--627}
}

@ARTICLE{BKSS94,
  author = {John A. Board Jr. and Laxmikant V. Kal{\'e} and Klaus Schulten and
	R.~D. Skeel and Tamar Schlick},
  title = {Modeling Biomolecules: Larger Scales, Longer Durations},
  journal = {IEEE Computational Science \& Engineering},
  year = {1994},
  volume = {1},
  pages = {19--30},
  ack = {GC},
  nack = {NSF/ARPA93}
}

@ARTICLE{Kalk94,
  author = {T. Kalkreuter},
  title = {Multigrid methods for the computation of propagators in gauge fields},
  journal = {Int. J. Mod. Phys. C, Phys. Comput.},
  year = {1994},
  volume = {5},
  pages = {629--700}
}

@ARTICLE{KARN93,
  author = {Pratima S. Karnik and Sucheta Kulkarni and Xiao--Pu Liu and G. Thomas
	Budd and Ronald M. Bukowski},
  title = {Estrogen Receptor Mutations in Tamoxifen--resistant Breast Cancer},
  journal = {Cancer research},
  year = {1994},
  volume = {54},
  pages = {349--353}
}

@BOOK{KlPS94,
  title = {Numerical Solution of SDE Through Computer Experiments},
  publisher = {Springer-Verlag},
  year = {1994},
  author = {P. E. Kloeden and E. Platen and H. Schurz},
  nremark = {in the title above, should SDE be Stochastic Differential Equations?},
  place = {Berlin}
}

@ARTICLE{KRAU94,
  author = {P.J. Kraulis and P.J. Domaille and S.L. Campbell-Burk and T. {Van
	Aken} and E.D. Laue},
  title = {Solution Structure and Dynamics of ras p21.{GDP} determined by heteronuclear
	three- and four-dimensional {NMR} spectroscopy},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {3515--3531}
}

@ARTICLE{KREU94,
  author = {A. Kreusch and A. Neubuser and E. Schiltz and J. Wechesser and G.E.
	Schulz},
  title = {Structure of the membrane channel porin from rhodopseudomonas blastica
	at 2.0 angstrom resolution},
  journal = {Protein Science},
  year = {1994},
  volume = {3},
  pages = {58--63}
}

@INPROCEEDINGS{KUHL94,
  author = {W. Kuhlbrandt},
  title = {High-Resolution Electron Crystallography of Membrane Proteins},
  booktitle = {Membrane Protein Structure: Experimental Approaches},
  year = {1994},
  editor = {S.H. White},
  pages = {206--223},
  address = {New York},
  publisher = {Oxford University press}
}

@ARTICLE{KUKI94,
  author = {M. Kuki and H. Nagae and R.J. Cogdell and Y. Koyama},
  title = {Solvent Effect on spheroidene in nonpolar and polar solutions and
	the environment of spheroidene in the light-harvesting complexes
	of {\em Rhodobacter sphaeroides} 2.4.1 as revealed by the energy
	of the (1)A(g)(-)B-1(U)+ absorption and the frequencies of the vibronically
	coupled C=C stretching Raman lines in the (1)A(G)(-) And 2(1)A(G)(-)
	states},
  journal = PCPB,
  year = {1994},
  volume = {59},
  pages = {116}
}

@ARTICLE{Kunt94,
  author = {Irwin D. Kuntz},
  title = {Theory and Simulation: Editorial Overview},
  journal = {Current Opinion in Structural Biology},
  year = {1994},
  volume = {4},
  pages = {231--233},
  nremark = {intro to collection of interesting articles; ``of outstanding interest''
	is the paper by holst and saied in J Comp Chem according to the "survey"
	article by Kim A Sharp in Current Opinion in Structural Biology 4:234--239
	(1994). Sharp cites 73 papers and designates only 4 as of outstanding
	interest}
}

@ARTICLE{KuMS94,
  author = {Irwin D. Kuntz and Elaine C. Meng and Brian K. Shoichet},
  title = {Structure-based molecular design},
  journal = {Accounts of Chemical Research},
  year = {1994},
  volume = {27},
  pages = {117--123},
  number = {5}
}

@ARTICLE{KUHL94a,
  author = {W. K{\"u}hlbrandt and D.N. Wang and Y. Fujiyoshi},
  title = {Atomic model of plant light-harvesting complex by electron crystallography},
  journal = NAT,
  year = {1994},
  volume = {367},
  pages = {614--621}
}

@ARTICLE{LADB94,
  author = {J.~E.~Ladbury and J.~G.~Wright and J.~M.~Sturtevant and P.~B.~Sigler},
  title = {A thermodynamic study of the trp repressor-operator interaction},
  journal = JMB,
  year = {1994},
  volume = {238},
  pages = {669--6681},
  annote = {hydrophobic surface area excluded by complex formation of GR with
	GRE}
}

@ARTICLE{LAMB94,
  author = {D. G. Lambright and J. P. Noel and H. E. Hamm and P. B. Sigler},
  title = {Structural determinants for activation of the $\alpha$-subunit of
	a heterotrimeric {G}-protein},
  journal = NAT,
  year = {1994},
  volume = {369},
  pages = {621--628}
}

@ARTICLE{LAMM94,
  author = {G.~Lamm and L.~Wong and G.~R.~Pack},
  title = {{M}onte {C}arlo and {P}oisson--{B}oltzmann Calculations of the Fraction
	of Counterions Bound to {DNA}},
  journal = BP,
  year = {1994},
  volume = {34},
  pages = {227--237},
  annote = {studies free and bound ions around {DNA}with MC and PB, PB suggests
	invariance of surface ion concentration as electrolyte is added and
	underestimates as compared to MC, PB indicate that amount of bound
	ion per phosphate is .67 and independent of salt concentration, MC
	agrees with condensation theory that .768 and .817 are the ion/phosphate
	for B-DNA and A-DNA using 2\AA hard sphere ions}
}

@ARTICLE{LANT94,
  author = {E. J. P. Lanthrop and R. A. Friesner},
  title = {Simulation of Optical Spectra from the Reaction Center of {\em Rb.
	sphaeroides}. Effects of an Internal Charge-Separated State of the
	Special Pair},
  journal = JPC,
  year = {1994},
  volume = {98},
  pages = {3056--3066}
}

@BOOK{LaMa94,
  title = {Chaos, Fractals, and Noise: Stochastic Aspects of Dynamics},
  publisher = {Springer-Verlag},
  year = {1994},
  author = {Andrzej Lasota and Michael C. Mackey},
  address = {New York},
  edition = {2nd},
  nremark = {... techniques presented, and the ideas in this book should thus prove
	useful in the study of a number of applied sciences. 472 PP./HARDCOVER/ISBN
	0-387-94049-9 APPLIED MATHEMATICAL SCIENCES, volume 97, LIST PRICE:
	$53.95$}
}

@ARTICLE{LECH94,
  author = {Lechner, R. E. and Dencher, N. A. and Fitter, J. and Dippel, T},
  title = {2-DIMENSIONAL PROTON DIFFUSION ON PURPLE MEMBRANE},
  journal = SSI,
  year = {1994},
  volume = {40},
  pages = {296--304}
}

@ARTICLE{LECK94,
  author = {D. E. Leckband and F. J. Schmitt and J. N. Israelachvili and W. Knoll},
  title = {Direct Force Measurements of Specific and Nonspecific Protein Interactions},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {4611--4624},
  number = {15}
}

@ARTICLE{LEE94,
  author = {D. Lee and G.J. Malpeli},
  title = {Global Form ans Singularity: Modeling the Blind Spot's Role in Lateral
	Geniculate Morphogenesis},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {1292--1294}
}

@ARTICLE{LEE-94,
  author = {Daeyeol Lee and Joseph G. Malpeli},
  title = {Global Form and Singularity: Modeling the Blind Spot's Role in Lateral
	Geniculate Morphogenesis},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {1292--1294}
}

@INBOOK{LEFS94,
  pages = {2842--2856},
  title = {Influence of a steroid receptor {DNA}--binding domain on transcriptional
	regulatory functions.},
  publisher = {Cold Spring Harbor Laboratory Press},
  year = {1994},
  author = {J.~A.~Lefstin and J.~R.~Thomas and K.~R.~Yamamoto},
  volume = {8},
  address = {UK},
  booktitle = {Genes and Development}
}

@ARTICLE{LeRe94,
  author = {B. Leimkuhler and S. Reich},
  title = {The Numerical Solution of Constrained {H}amiltonian Systems},
  journal = {Math.\ Comput.},
  year = {1994},
  volume = {63},
  pages = {589--605},
  nremark = {Also technical report SC-92-16, Konrad-Zuse-Zentrum f\"ur Informationstechnik
	Berlin, Berlin, Germany, year=1992}
}

@ARTICLE{LeSk94,
  author = {B. Leimkuhler and R.~D. Skeel},
  title = {Symplectic numerical integrators in constrained {H}amiltonian systems},
  journal = {J. Comput. Phys.},
  year = {1994},
  volume = {112},
  pages = {117--125},
  number = {1},
  nack = {NSF90}
}

@ARTICLE{LIAN94,
  author = {Tianquan Lian and Bruce Locke and Yuriy Kholodenko and Robin M. Hochstrasser},
  title = {Energy Flow from Solute to Solvent Probed by Femtosecond IR Spectroscopy:
	Malachite Green and Heme Protein Solutions},
  journal = JPC,
  year = {1994},
  volume = {98},
  pages = {11648--11656}
}

@INPROCEEDINGS{lin:atm,
  author = {Mengjou Lin and Jenwei Hsieh and David H. C. Du and Joseph P. Thomas
	and James A. MacDonald},
  title = {Distributed Network Computing Over Local {ATM} Networks},
  booktitle = {Proceedings of Supercomputing '94},
  year = {1994},
  pages = {154--163},
  address = {Washington, DC},
  publisher = {IEEE Computer Society Press}
}

@ARTICLE{LINK94,
  author = {W. Linke and V. Popov and G. Pollack},
  title = {Passive and active tension in single cardiac myofibrils},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {782--792}
}

@ARTICLE{LOCK94,
  author = {A. Lockhart and R.A. Cross},
  title = {Origins of reversed directionality in the ncd molecular motor},
  journal = EMBO,
  year = {1994},
  volume = {13},
  pages = {751--757}
}

@ARTICLE{LOUN94,
  author = {V. Lounnas and B. M. Pettitt and G. N. Phillips},
  title = {A Global Model of the Protein-Solvent Interface},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {601--614}
}

@ARTICLE{LUCH94,
  author = {J. Luchoomun and N. Theret and V. Clavey and P. Duchateau and M.
	Rosseneu and R. Brasseur and P. Denefle and J.-C. Fruchart and G.
	R. Castro},
  title = {Structural Domain of Apolipoprotein {A-I} Involved in its Interaction
	with Cells},
  journal = BBA,
  year = {1994},
  volume = {1212},
  pages = {319--326}
}

@ARTICLE{LUND94,
  author = {T.~Lundb{\"a}ck and J.~Zilliacus and J.~A.~Gustafsson and J.~Carlstedt-Duke
	and T.~H{\"a}rd},
  title = {Thermodynamics of sequence-specific glucocorticoid receptor--{DNA}
	interactions.},
  journal = BCHJ,
  year = {1994},
  volume = {33},
  pages = {5955--5965}
}

@ARTICLE{LDTV94,
  author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
  title = {A comparison of particle-particle, particle-mesh and {E}wald methods
	for calculating electrostatic interactions in periodic molecular
	systems},
  journal = {Molecular Simulation},
  year = {1994},
  volume = {14},
  pages = {11--20}
}

@ARTICLE{MAED94,
  author = {A. Maeda and J. Sasaki and Y. Yamazaki and R. Needleman and J. K.
	Lanyi},
  title = {Interaction of Aspartate-85 with a Water Molecule and the Protonated
	{Schiff} Base in the {L} Intermediate of Bacteriorhodopsin -- A {Fourier}-Transform
	Infrared Spectroscopic Study.},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {1713--1717}
}

@ARTICLE{MALI94,
  author = {B.P. Maliwal and B.-Z. Yu and H. Szmacinski and T. Squier and J.
	van Binsbergen and A.J. Slotboom and M.K. Jain},
  title = {Functional Significance of the Conformational dynamics of the N-Terminal
	segment of secreted phospholipase {A$_2$} at the interface},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {4506--4516}
}

@ARTICLE{MaFl94,
  author = {Costas D. Maranas and Christodoulos A. Floudas},
  title = {Global Minimum Potential Energy Conformations of Small Molecules},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {135--170},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{MARK94,
  author = {John F. Marko and Eric D. Siggia},
  title = {Fluctuations and Supercoiling of {DNA}},
  journal = SCI,
  year = {1994},
  volume = {265},
  pages = {506--508}
}

@ARTICLE{MART94C,
  author = {C. Martin and K. Freed},
  title = {{\it Ab initio} Computation of Semiempirical {$\pi$}-electron methods.
	III. The benzene Molecule, the Zero-Differential-Overlap Approximation,
	and the Tranferability of Parameters.},
  journal = JCP,
  year = {1994},
  volume = {101},
  pages = {5929--5941}
}

@ARTICLE{Mart94,
  author = {G.~J. Martyna},
  title = {Remarks on `Constant-Temperature Molecular Dynamics with Momentum
	Conservation'},
  journal = {Phys.\ Rev.~E},
  year = {1994},
  volume = {50},
  pages = {3234--3236},
  number = {4}
}

@ARTICLE{MART94A,
  author = {G. J. Martyna and D.~J. Tobias and M. L. Klein},
  title = {Constant Pressure Molecular Dynamics Algorithms},
  journal = JCP,
  year = {1994},
  volume = {101},
  pages = {4177--4189},
  number = {5}
}

@ARTICLE{MaTK94,
  author = {Glenn J. Martyna and Douglas J. Tobias and Michael L. Klein},
  title = {Constant pressure molecular dynamics algorithms},
  journal = JCP,
  year = {1994},
  volume = {101},
  pages = {4177--4189},
  number = {5},
  annote = {Algortims for constant pressure and constant tempurature isotropic
	volume fluctuations and fully flexible simulations cells}
}

@ARTICLE{MARU94,
  author = {K. Maruyama},
  title = {Connectin, an elastic protein of striated muscle},
  journal = BPC,
  year = {1994},
  volume = {50},
  pages = {73--85}
}

@INPROCEEDINGS{MaSa94,
  author = {T.~H. Massie and J.~K. Salisbury},
  title = {The {PHANTOM} haptic interface: {A} device for probing virtual objects},
  booktitle = {ASME Winter Annual Meeting},
  year = {1994},
  volume = {55},
  series = {Dynamic Systems and Control Division},
  pages = {295--299}
}

@ARTICLE{MCCO94,
  author = {K.~J.~ McConnell and R.~Nirmala and M.~A.~Young and G.~Ravishanker
	and D.~L.~Beveridge},
  title = {A Nanosecond Molecular Dynamics Trajectory for a {B-DNA} Double Helix:
	Evidence for Substates},
  journal = JACS,
  year = {1994},
  volume = {116},
  pages = {4461--4462},
  annote = {3 simulations of d({CGCGAATTCGCG}) dodecamer 2 at 500ps and 1ns,
	watson crick bp constraints with gromos, 7.5 to 11.5\AA cut-off,
	.25 charge phosphates, 3500 waters, constant volume, period boundaries,
	THIS IS JUST A COMMUNICATION TO THE EDITOR}
}

@ARTICLE{McTh94,
  author = {I. K. McDonald and J. M. Thornton},
  title = {Satisfying Hydrogen Bonding Potential in Proteins},
  journal = {J.\ Mol.\ Biol.},
  year = {1994},
  volume = {238},
  pages = {777--793}
}

@ARTICLE{MERC94,
  author = {M. Merchan and E. Orti and B. Roos},
  title = {Theoretical Determination of the Electronic Spectrum of Free Base
	Porphin.},
  journal = CPL,
  year = {1994},
  volume = {226},
  pages = {27--36}
}

@ARTICLE{MERR94,
  author = {E. A. Merritt and M. E. P. Murphy},
  title = {{Raster3D} Version 2.0 - A Program for Photorealistic Molecular Graphics},
  journal = ACD,
  year = {1994},
  volume = {50},
  pages = {869--873}
}

@ARTICLE{MILL94,
  author = {R.J. Dwayne Miller},
  title = {Energetics and Dynamics of Deterministic Protein Motion},
  journal = ACR,
  year = {1994},
  volume = {27},
  pages = {145--150}
}

@ARTICLE{MONG94,
  author = {A. Monge and R. Friesner and B. Honig},
  title = {An Algorith to Generate Low-Resolution Protein Tertiary Structures
	from Knowledge of Secondary Structures},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {5027--5029}
}

@ARTICLE{MORG94,
  author = {JE. Morgan and MI. Verkhovsky and M. Wikstr{\"o}m},
  title = {The Histidine Cycle - A New Model For Proton Translocation In the
	Respiratory Heme-copper Oxidases.},
  journal = {Journal of Bioenergetics And Biomembranes},
  year = {1994},
  volume = {26},
  pages = {599--608},
  number = {6}
}

@ARTICLE{MOY94,
  author = {Vincent T. Moy and Ernst-Ludwig Florin and Hermann E. Gaub},
  title = {Intermolecular Forces and Energies Between Ligands and Receptors},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {257--259},
  annote = {june 1}
}

@ARTICLE{MOY94A,
  author = {Vincent T. Moy and Ernst-Ludwig Florin and Hermann E. Gaub},
  title = {Adhesive forces between ligand and receptor measured by {AFM}},
  journal = CAS,
  year = {1994},
  volume = {93},
  pages = {343--348},
  annote = {june 1}
}

@ARTICLE{MULL94,
  author = {Yves A. Muller and Mark H. Ultsch and Robert F. Kelley and Abraham
	M. {de\,Vos}},
  title = {Structure of the Extracellular Domain of Human Tissue Factor: Location
	of the Factor {VII}a Binding Site},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {10864--10870}
}

@ARTICLE{MUSG94,
  author = {E.~A.~Musgrove and R.~L.~Sutherland},
  title = {Cell cycle control by steroid hormones},
  journal = {CBIO},
  year = {1994},
  volume = {5},
  pages = {381--389}
}

@ARTICLE{NaKV94,
  author = {A. Nakano and R. K. Kalia and P. Vashishta},
  title = {Multiresolution Molecular Dynamics Algorithm for Realistic Materials
	Modeling on Parallel Computers},
  journal = CPC,
  year = {1994},
  volume = {83},
  pages = {197--214},
  number = {2}
}

@ARTICLE{Neal94,
  author = {Radford M. Neal},
  title = {An Improved Acceptance Procedure for the Hybrid {M}onte {C}arlo Algorithm},
  journal = JCMP,
  year = {1994},
  volume = {111},
  pages = {194--203}
}

@ARTICLE{NER94,
  author = {S. S. Ner and A. A. Travers},
  title = {{HMG-D}, the {{\em Drosophila melanogaster}} homologue of {HMG 1}
	protein, is associated with early embryonic chromatin in the absence
	of histone {H1}},
  journal = EMBO,
  year = {1994},
  volume = {13},
  pages = {1817--1822},
  number = {8}
}

@ARTICLE{NER94a,
  author = {S. S. Ner and A. A. Travers and M. E. A. Churchill},
  title = {Harnessing the writhe: a role for {DNA} chaperons in nucleoprotein-complex
	formation},
  journal = TIBS,
  year = {1994},
  volume = {19},
  pages = {185--187}
}

@ARTICLE{NiTa94,
  author = {Christoph Niedereiter and P. Tavan},
  title = {A structure adapted multipole method for electrostatic interactions
	in protein dynamics},
  journal = {J. Chem.\ Phys.},
  year = {1994},
  address = {?????Eingesandt}
}

@ARTICLE{NORB94,
  author = {J. Norberg and L. Nilsson},
  title = {High pressure molecular dynamics of a nucleic acid fragment},
  journal = CPL,
  year = {1994},
  volume = {224},
  pages = {219--224}
}

@ARTICLE{NORR94,
  author = {B.J. Norris and D.J. Miller},
  title = {Nucleotide sequence of a c{DNA} clone encoding the precursor of the
	peridinin-chlorophyll a-binding protein from the dinoflagellate symbiodinium
	{SP}},
  journal = {Plant Mol.\ Biol.},
  year = {1994},
  volume = {24},
  pages = {673--677}
}

@ARTICLE{ObTu94,
  author = {S.A. Oberlender and R.S. Tuan},
  title = {Expression and functional involvement of {N}-cadherin in embryonic
	limb chondrogenesis},
  journal = {Development},
  year = {1994},
  volume = {120},
  pages = {177--187}
}

@ARTICLE{OkSk94a,
  author = {D. Okunbor and R.~D. Skeel},
  title = {Canonical numerical methods for molecular dynamics simulations},
  journal = {J. Comput. Chem.},
  year = {1994},
  volume = {15},
  pages = {72--79},
  number = {1},
  nack = {NSF90, NIH92}
}

@ARTICLE{OkSk94b,
  author = {D. Okunbor and R.~D. Skeel},
  title = {Canonical Runge-Kutta-Nystrom methods of orders 5 and 6},
  journal = {J. Comp. Appl. Math.},
  year = {1994},
  volume = {51},
  pages = {375--382}
}

@ARTICLE{OLIV94,
  author = {M. Olivucci and F. Bernardi and P. Celani and I. Ragazos and M. A.
	Robb},
  title = {Excited-State Cis-Trans Isomerization of {\it cis}-Hexatriene. A
	{CAS-SCF} Computational Study},
  journal = JACS,
  year = {1994},
  volume = {116},
  pages = {1077--1085}
}

@ARTICLE{OLIV94B,
  author = {M. Olivucci and F. Bernardi and S. Ottani and M. A. Robb},
  title = {Substituent Effects in Buta-1,3-diene Photochemistry: A {CAS-SCF}
	Study of 2,3-Dimethylbutadiene and 2-Cyanobutadiene Excited-State
	Reaction Paths},
  journal = JACS,
  year = {1994},
  volume = {116},
  pages = {2034--2048}
}

@ARTICLE{ONG94,
  author = {S. Ong and S.J. Cai and C. Bernal and D. Rhee and X. Qiu and C. Pidgeon},
  title = {Phospholipid Immobilization on Solid Surfaces},
  journal = {Analytical Chemistry},
  year = {1994},
  volume = {66},
  pages = {782--792}
}

@ARTICLE{OPSA94,
  author = {L.R. Opsahl and W.W. Webb},
  title = {Lipid-glass adhesion in giga-sealed patch-clamped membranes},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {75--79},
  annote = {relation of radius of curvature to tension and pressure}
}

@BOOK{OUST94,
  title = {{Tcl} and the {Tk} Toolkit},
  publisher = {Addison-Wesley},
  year = {1994},
  author = {J. Ousterhout},
  address = {Reading, Massachusetts}
}

@BOOK{PAIN94,
  title = {Mechanisms of Protein Folding},
  publisher = {Oxford University Press},
  year = {1994},
  author = {R. H. Pain},
  address = {New York}
}

@ARTICLE{PaSX94,
  author = {Panos M. Pardalos and David Shalloway and Guoliang Xue},
  title = {Optimization Methods for Computing Global Minima of Nonconvex Potential
	Energy Functions},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {117--133},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@INPROCEEDINGS{PAST94,
  author = {R. W. Pastor},
  title = {Techniques and Applications of {L}angevin Dynamics Simulations},
  booktitle = {The Molecular Dynamics of Liquid Crystals},
  year = {1994},
  editor = {G. R. Luckhurst and C. A. Veracini},
  pages = {85--138},
  address = {the Netherlands},
  publisher = {Kluwer}
}

@ARTICLE{PERS94B,
  author = {A. Persechini and K. McMillan and P. Leakey},
  title = {Activation of myosin light chain kinase and nitric oxide synthase
	activities by calmodulin fragments},
  journal = JBC,
  year = {1994},
  volume = {269},
  pages = {16148--16154}
}

@ARTICLE{PERS94,
  author = {B. Persson and P. Argos},
  title = {Prediction of transmembrane segments in proteins utilising multiple
	sequence alignments},
  journal = JMB,
  year = {1994},
  volume = {237},
  pages = {182}
}

@ARTICLE{PhRo94,
  author = {Andrew T. Phillips and J. B. Rosen},
  title = {A Quadratic Assignment Formulation of the Molecular Conformation
	Problem},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {229--241},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{PICO94,
  author = {Daniel Picot and Patrick J. Loll and Michael Garavito},
  title = {The {X}-ray Crystal Structure of the Membrane Protein Prostaglandin
	{$H_2$} Synthase-1},
  journal = NAT,
  year = {1994},
  volume = {367},
  pages = {243--249},
  number = {20}
}

@ARTICLE{PICO94A,
  author = {R.~Picot and R.~M.~Garavito},
  title = {{Prostaglandin H synthase: implications for membrane structure}},
  journal = FEBS,
  year = {1994},
  volume = {346},
  pages = {21--25},
  number = {1}
}

@ARTICLE{PIDG94,
  author = {C. Pidgeon and S. Ong and H. Choi},
  title = {Preparation of mixed ligand immobilized artificial membranes for
	predicting drug binding to membranes},
  journal = {Analytical Chemistry},
  year = {1994},
  volume = {66},
  pages = {2701--2709}
}

@ARTICLE{POLI94,
  author = {A. Politou and M. Gautel and M. Pfuhl and S. Labeit and A. Pastore},
  title = {Immunoglobulin-type domains of titin: same fold, different stability?},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {4730--4737}
}

@ARTICLE{PONT94,
  author = {A. Pontiggia and R. Rimini and V. R. Harley and P. N. Goodfellow
	and R. L. Lovell-Badge and M. E. Bianchi},
  title = {Sex-reversing mutations affect the architecture of {SRY-DNA} complexes},
  journal = EMBO,
  year = {1994},
  volume = {13},
  pages = {6115--6124},
  number = {24}
}

@INPROCEEDINGS{POPO94,
  author = {J.L. Popot and C. de Vitry and A. Atteia},
  title = {Folding and assembly of integral membrane proteins: An introduction},
  booktitle = {Membrane Protein Structure: Experimental Approaches},
  year = {1994},
  editor = {S.H. White},
  pages = {41},
  address = {New York},
  publisher = {Oxford University press}
}

@ARTICLE{PUGL94,
  author = {Luisa Pugliese and Alessandro Coda and Massimo Malcovati and Martino
	Bolognesi},
  title = {Crystal Structure of Apo-avidin from Hen Egg-white},
  journal = JMB,
  year = {1994},
  volume = {235},
  pages = {42--46},
  annote = {june 1}
}

@ARTICLE{PULL94,
  author = {T. Pullerits and K. J. Visscher and S. Hess and V. Sundstr{\"o}m
	and A. Freiberg and K. Timpmann},
  title = {Energy Transfer in the Inhomogeneously Broadened Core Antenna of
	Purple Bacteria: A Simultaneous Fit of Low-Intensity Picosecond Absorption
	and Fluorescence Kinetics},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {236--248}
}

@ARTICLE{PUET94,
  author = {Benno P{\"u}tz and Daniel Barsky and Klaus Schulten},
  title = {Mechanisms of Liposomal Contrast Agents in Magnetic Resonance Imaging.},
  journal = JLSR,
  year = {1994},
  volume = {4},
  pages = {771--808},
  number = {2},
  annote = {Invited for publication. Submitted approx. Oct 25, 1993 to Journal
	of Liposome Research.},
  tbtechrep = {TB-93-08}
}

@ARTICLE{RAMA94,
  author = {V.~Ramakrishnan},
  title = {Histone structure.},
  journal = COSB,
  year = {1994},
  volume = {4},
  pages = {44--50}
}

@ARTICLE{READ94,
  author = {C. M. Read and P. D. Cary and N. S. Preston and M. Lnenicek-Allen
	and C. {Crane-Robinson}},
  title = {The {DNA} sequence specificity of {HMG} boxes lies in the minor wing
	of the structure},
  journal = EMBO,
  year = {1994},
  volume = {13},
  pages = {5639--5646},
  number = {23}
}

@TECHREPORT{REIC94,
  author = {S. Reich},
  title = {Numerical Integration of Highly Oscillatory {H}amiltonian Systems
	Using Slow Manifolds},
  institution = {University of Illinois},
  year = {1994},
  type = {Beckman Institute Technical Report},
  number = {TB-94-06},
  tbtechrep = {TB-94-06}
}

@TECHREPORT{REIC94A,
  author = {S. Reich},
  title = {Smoothed Dynamics of Highly Oscillatory {H}amiltonian Systems},
  institution = {University of Illinois},
  year = {1994},
  type = {Beckman Institute Technical Report},
  number = {TB-94-12},
  note = {Preprint; also Reich, S., Molecular dynamics with soft constraints},
  annote = {submitted to Physica D - Phys. Rev. D ?},
  tbtechrep = {TB-94-12}
}

@ARTICLE{RICE94,
  author = {Luke M. Rice and Axel T. Br{\"u}nger},
  title = {Torsion Angle Dynamics: Reduced Variable Conformational Sampling
	Enhances Crystallographic Structure Refinement},
  journal = PRO,
  year = {1994},
  volume = {19},
  pages = {277--290}
}

@ARTICLE{RoSc94,
  author = {J. E. Roberts and J. Schnitker},
  title = {{H}ow the unit cell surface charge distribution affects the energetics
	of ion-solvent interactions in simulations},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {101},
  pages = {5024}
}

@ARTICLE{ROST94,
  author = {B. Rost and C. Sander and R. Schneider},
  title = {{PHD} - An Automatic Mail Server for Protein Secondary Structure
	Prediction},
  journal = {Computer Applications In The Biosciences},
  year = {1994},
  volume = {10},
  pages = {53}
}

@ARTICLE{RZEP94,
  author = {S. Rzepa and B. J. Whitaker and M. J. Winter},
  title = {Chemical Applications of the {World-Wide-Web} System},
  journal = {J.~Chem.\ Soc.,\ Chem.~Commun.},
  year = {1994},
  pages = {1907},
  note = {{\tt http://www.ch.ic.ac.uk/rzepa/RSC/CC/4\_02963A.html}}
}

@TECHREPORT{SaTr94,
  author = {Prasenjit Saha and Scott Tremaine},
  title = {Long-term planetary integration with individual time steps},
  year = {1994},
  number = {CITA-94-10},
  remark = {bodies are not synchronized at interaction times}
}

@ARTICLE{Sait94,
  author = {Minoru Saito},
  title = {Molecular Dynamics Simulations of Protein in Solution: Artifacts
	Caused by Cutoff Approximation},
  journal = {J.Chem.\ Phys.},
  year = {1994},
  volume = {101},
  number = {5}
}

@ARTICLE{SaKi94,
  author = {Salerno, M. and Y.S. Kivshar},
  title = {DNA promoters and nonlinear dynamics},
  journal = {PHYSICS LETTERS A},
  year = {1994},
  volume = {193},
  pages = {263},
  number = {3}
}

@ARTICLE{SAMP94,
  author = {R. Sampogna and B. Honig},
  title = {Environmental Effects on the Protonation States of Active Site Residues
	in Bacteriorhodopsin},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {1341--1352}
}

@ARTICLE{SANC94,
  author = {A. Sancar},
  title = {Structure and Function of {D}{N}{A} Photolyase},
  journal = {Biochem.},
  year = {1994},
  volume = {33},
  pages = {2--9}
}

@BOOK{SaCa94,
  title = {Numerical {H}amiltonian Problems},
  publisher = {Chapman and Hall},
  year = {1994},
  author = {J.~M. San{z-S}erna and M.~P. Calvo},
  address = {London},
  isbn = {0-412-54290-0},
  nremark = {The purpose of the book is to present a unified introduction to the
	interdisciplinary and growing field of symplectic integration of
	Hamiltonian problems. It includes five preliminary chapters on Hamiltonian
	problems and numerical methods, so that little background knowledge
	should be required. Numerical examples are provided throughout,\$48.50,
	207 pp.}
}

@ARTICLE{SASA94,
  author = {J. Sasaki and J. K. Lanyi and R. Needleman and T. Yoshizawa and A.
	Maeda},
  title = {Complete identification of {C=O} stretching vibrational bands of
	protonated aspartic acid residues in the difference infrared spectra
	of {M} and {N} intermediates versus bacteriorhodopsin.},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {3178--3184}
}

@ARTICLE{SUGT94,
  author = {M. Sato-Maeda and M. uchida and F. Graner and H. Tashiro},
  title = {Quantitative evaluation of tissue specific cell adhesion at the level
	of a single cell pair},
  journal = {Dev. Biol.},
  year = {1994},
  volume = {162},
  pages = {77--84}
}

@ARTICLE{SCHA94,
  author = {C. Scharnagl and J. Hettenkofer and S. F. Fischer},
  title = {Proton Release Pathway in Bacteriorhodopsin: Molecular Dynamics and
	Electrostatic Calculations},
  journal = {Int.\ J.\ Quantum Chem.},
  year = {1994},
  volume = {21},
  pages = {33--56}
}

@ARTICLE{SCHL94,
  author = {T. Schlick and B. Li and W. Olson},
  title = {The influence of salt on the structure and energetics of supercoiled
	{DNA}},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {2146--2166}
}

@ARTICLE{SCHL94a,
  author = {T. Schlick and W. Olson and T. Westcott and J. P. Greenberg},
  title = {On higher buckling transitions in supercoiled {DNA}},
  journal = BP,
  year = {1994},
  volume = {34},
  pages = {565--597}
}

@ARTICLE{SCHN94,
  author = {T. Schneider and H.-P. Thalau and P. Semm and W. Wiltschko},
  title = {Melatonin is crucial for the migratory orientation of pied flycatchers
	{\em {F}icedula hyopoluca pallas}},
  journal = {J.~Exp.~Biol.},
  year = {1994},
  volume = {194},
  pages = {255--262}
}

@ARTICLE{Schu94,
  author = {K. Schulten},
  title = {Dynamics under influence of Stochastic Forces},
  journal = {???},
  year = {1994}
}

@ARTICLE{SCHU94A,
  author = {Maria A. Schumacher and Kang Yell Choi and Howard Zalkin and Richard
	G. Brennan},
  title = {Crystal structure of {LacI} member, {PurR}, bound to {DNA}: {Minor}
	groove binding by $\alpha$ helices},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {763--770}
}

@ARTICLE{SCHW94,
  author = {Ulrike Schweiger and J{\"o}rg Tittor and Dieter Oesterhelt},
  title = {Bacteriorhodopsin Can Function without a Covalent Linkage Between
	Retinal and Protein},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {535--541}
}

@ARTICLE{SCOT94,
  author = {D. L. Scott and A.M. Mandel and B. Honig},
  title = {The electrostatic basis for the interfacial binding of secretory
	{P}hospholipases {A}$_2$},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {493--504}
}

@ARTICLE{SELT94,
  author = {S. Seltzer},
  title = {13-ACETOXY-13-DESMETHYLRETINAL - SYNTHESIS, INCORPORATION INTO BACTERIORHODOPSIN,
	AND ITS APPARENT INACTIVATING EFFECT},
  journal = JACS,
  year = {1994},
  volume = {116},
  pages = {9383--9384}
}

@MISC{stl,
  author = {SGI},
  title = {The {S}tandard {T}emplate {L}ibrary},
  year = {1994},
  note = {{\small \texttt{http://www.sgi.com/tech/stl}}}
}

@ARTICLE{SHAK94,
  author = {Z.~Shaked and G.~Guzikevich-Guerstein and F.~Frolow and D.~Rabinovich
	and A.~Joachimiak and P.~B.~Sigler},
  title = {Determinants of repressor/operator recognition from the structure
	of the {\em trp} operator binding site.},
  journal = NAT,
  year = {1994},
  volume = {368},
  pages = {469--473},
  annote = {it's actually a letter to nature}
}

@ARTICLE{SHI94,
  author = {Yaoming Shi and John E. Hearst},
  title = {The {Kirchhoff} elastic rod, the nonlinear {Schr\"odinger} equation,
	and {DNA} supercoiling},
  journal = JCP,
  year = {1994},
  volume = {101},
  pages = {5186--5200},
  number = {6}
}

@ARTICLE{ShKT94,
  author = {J. Shimada and H. Kaneko and T. Takada},
  title = {Performance of Fast Multipole Methods for Calculating Electrostatic
	Interactions in Biomacromolecular Simulations},
  journal = JCC,
  year = {1994},
  volume = {15},
  pages = {28},
  number = {1}
}

@ARTICLE{SINH94,
  author = {Amitabh B. Sinha and Klaus Schulten and Helmut Heller},
  title = {Performance Analysis of a Parallel Molecular Dynamics Program},
  journal = CPC,
  year = {1994},
  volume = {78},
  pages = {265--278},
  tbtechrep = {TB-92-13}
}

@ARTICLE{SkBi94,
  author = {R.~D. Skeel and J. J. Biesiadecki},
  title = {Symplectic integration with variable stepsize},
  journal = {Annals of Numer. Math.},
  year = {1994},
  volume = {1},
  pages = {191--198},
  nack = {NSF90, NIH92},
  nremark = {introduces artificial splittings}
}

@ARTICLE{SOMS94,
  author = {O. J. G. Somsen and F. {van Mourik} and R. {van Grondelle} and L.
	Valkunas},
  title = {Energy Migration and Trapping in a Spectrally and Spatially Inhomogeneous
	Light-Harvesting Antenna},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {1580--1596}
}

@ARTICLE{SpMa94,
  author = {Jerome Spanier and Earl H. Maize},
  title = {Quasi-Random Methods for Estimating Integrals Using Relatively Small
	Samples},
  journal = {SIAM Review},
  year = {1994},
  volume = {36},
  pages = {18--44},
  number = {1}
}

@ARTICLE{SPOL94,
  author = {R.~S.~Spolar and M.~T.~Record},
  title = {Coupling of local folding to site-specific binding of proteins to
	{DNA}.},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {777--784}
}

@ARTICLE{SPUD94,
  author = {J. L. Spudich},
  title = {Protein-Protein Interaction Converts a Proton Pump into a Sensory
	Receptor},
  journal = {Cell},
  year = {1994},
  volume = {79},
  pages = {447--450}
}

@ARTICLE{StBr94,
  author = {P. J. Steinbach and B. R. Brooks},
  title = {New Spherical-Cutoff Methods for Long-range Forces in Macromolecular
	Simulation},
  journal = JCC,
  year = {1994},
  volume = {15},
  pages = {667--683}
}

@ARTICLE{STEI94,
  author = {G. Steinberg and M. Sheves and S. Bressler and M. Ottolenghi},
  title = {Factors affecting the formation of an {M}-like intermediate in the
	photocycle of 13-cis-bacteriorhodopsin},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {12439--12450}
}

@ARTICLE{STEM94,
  author = {W.~P.~Stemmer},
  title = {{DNA} shuffling by random fragmentation and reassembly: {\it In vitro}
	recombination for molecular evolution},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {10747--10751},
  annote = {method of reassembly of genes from random {DNA} fragments is reported}
}

@ARTICLE{StRT94,
  author = {J. E. Straub and A. B. Rashkin and D. Thirumalai},
  title = {Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide
	and Ribonuclease A},
  journal = {J. Am. Chem.},
  year = {1994},
  volume = {116},
  pages = {2049},
  number = {5}
}

@ARTICLE{STRA94,
  author = {J.~K.~Strauss and L.~J.~Maher {III}},
  title = {{DNA} Bending by Asymmetric Phosphate Neutralization},
  journal = SCI,
  year = {1994},
  volume = {266},
  pages = {1829--1834},
  annote = {neutralization of phosphates by protein (cations) or elsewise leads
	to a bending of the {DNA} towards the neutral site, this differs
	from the direction of bend found my GR-GRE simulations}
}

@ARTICLE{STRO94,
  author = {M. Stros and J. Strokova and J. O. Thomas},
  title = {{DNA} looping by the {HMG}-box domains of {HMG1} and modulation of
	{DNA} binding by the acidic {C}-terminal domain},
  journal = NAR,
  year = {1994},
  volume = {22},
  pages = {1044},
  number = {6}
}

@ARTICLE{StHu94,
  author = {A. M. Stuart and A. R. Humphries},
  title = {Model Problems in Numerical Stability Theory for Initial Value Problems},
  journal = {SIAM Review},
  year = {1994},
  volume = {36},
  pages = {226--257}
}

@ARTICLE{SUDA94,
  author = {H. Suda and M. Saito},
  title = {Molecular dynamics simulations for actin monomers in solution},
  journal = JTB,
  year = {1994},
  volume = {171},
  pages = {347--349}
}

@ARTICLE{SUDA94a,
  author = {Sucha Sudarsanam and Carl J. March and Subhashini Srinivasan},
  title = {Homology modeling of divergent proteins},
  journal = JMB,
  year = {1994},
  volume = {241},
  pages = {143--149}
}

@ARTICLE{SUKH94A,
  author = {S. I. Sukharev and P. Blount and B. Martinac and F. R. Blattner and
	and C. Kung},
  title = {A large-conductance machanosensitive channel in {\it E. coli} encoded
	by {\it mscL} alone},
  journal = NAT,
  year = {1994},
  volume = {368},
  pages = {265--268},
  annote = {First cloning of a MscL channel}
}

@ARTICLE{SUKH94,
  author = {S. I. Sukharev and B. Martinac and P. Blount and C. Kung},
  title = {Functional reconstitution as an assay for biochemical isolation of
	channel proteins: application to the molecular identification of
	a bacterial mechanosensitive channel},
  journal = {Methods: a {Companion} to {Methods} in {Enzymology}},
  year = {1994},
  volume = {6},
  pages = {51--59}
}

@ARTICLE{SUNG94,
  author = {Shen-Shu Sung},
  title = {Helix Folding Simulations with Various Initial Conformations},
  journal = BJ,
  year = {1994},
  volume = {66},
  pages = {1796--1803}
}

@ARTICLE{Suri94,
  author = {Suris, Y.B.},
  title = {A family of integrable symplectic standard-like maps related to symmetric
	spaces},
  journal = {PHYSICS LETTERS A},
  year = {1994},
  volume = {192},
  pages = {9--16},
  number = {1}
}

@ARTICLE{SURL94,
  author = {M. C. Surles and J. S. Richardson and D. C. Richardson and F. P.
	Brooks},
  title = {Sculpting Proteins Interactively: Continual Energy Minimization Embedded
	in a Graphical Modeling System},
  journal = PS,
  year = {1994},
  volume = {3},
  pages = {198--210}
}

@ARTICLE{SUZU94,
  author = {M.~Suzuki},
  title = {A framework for {DNA}--protein recognition code of the probe helix
	in transcription factors: the chemical and stereochemical rules.},
  journal = STR,
  year = {1994},
  volume = {2},
  pages = {317--326}
}

@ARTICLE{SVOB94,
  author = {Karel Svoboda and Steven M. Block},
  title = {Force and Velocity Measured for Single Kinesin Molecules},
  journal = CEL,
  year = {1994},
  volume = {77},
  pages = {773--784}
}

@ARTICLE{SWAI94,
  author = {M.~G.~Swain and M.~Maric},
  title = {Prevention of Immune--Mediated Arthritis in Cholestatic Rats: Involvement
	of Endogenous Glucocorticoids},
  journal = {Gastroenterology},
  year = {1994},
  volume = {107},
  pages = {1469--1474},
  number = {5},
  annote = {high-circulating glucocorticoids levels result in a relative state
	of immuno-suppression in BDR rats (BDR=bile-duct resected), immuno-suppresion
	is related to arthiritis}
}

@ARTICLE{TAKE94,
  author = {H. Takei and Y. Gat and Z. Rothman and A. Lewis and M. Sheves},
  title = {ACTIVE SITE LYSINE BACKBONE UNDERGOES CONFORMATIONAL CHANGES IN THE
	BACTERIORHODOPSIN PHOTOCYCLE},
  journal = JBC,
  year = {1994},
  volume = {269},
  pages = {7387--7389}
}

@ARTICLE{TANN94,
  author = {D. Tannor and B. Marten and R. Murphy and R. Friesner and D. Sitkoff
	and A. Nicholls and M. Rignalda and W. Doddard and B. Honig},
  title = {Accurate First Principles Calculation of Molecular Charge Distributions
	and Solvation Energies from Ab Initio Quantum Mechanics and Continium
	Dielectric Theory.},
  journal = JACS,
  year = {1994},
  volume = {116},
  pages = {11875--11882}
}

@ARTICLE{TITT94,
  author = {J. Tittor and U. Schweiger and D. Oesterhelt and E. Bamberg},
  title = {Inversion of Proton Translocation in Bacteriorhodopsin Mutants {D85N},
	{D85T}, and {D85,96N}},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {1682--1690},
  number = {4}
}

@ARTICLE{TOBI94A,
  author = {Irwin Tobias and Bernard D. Coleman and Wilma Olson},
  title = {The dependence of {DNA} tertiary structure on end conditions: {T}heory
	and implications for topological transitions},
  journal = JCP,
  year = {1994},
  volume = {101},
  pages = {10990--10996},
  number = {12}
}

@ARTICLE{TRAV94,
  author = {A. A. Travers and S. S. Ner and M. E. A. Churchill},
  title = {{DNA} chaperones: {A} solution to a persistence problem?},
  journal = {Cell},
  year = {1994},
  volume = {77},
  pages = {167--169}
}

@ARTICLE{TREI94,
  author = {D. K. Treiber and X. Zhai and H.-M. Jantzen and J. M. Essigman},
  title = {Cisplatin-{DNA} adducts are molecular decoys for the ribosomal {RNA}
	transcription factor {hUBF} (human upstream binding factor)},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {5672--5676}
}

@ARTICLE{TrTr94,
  author = {M. V. Tret'yakov and S. V. Tret'jakov},
  title = {Numerical integration of {H}amiltonian systems with external noise},
  journal = {Physics Letters A},
  year = {1994},
  volume = {194},
  pages = {371--374},
  issue = {5 and~6}
}

@ARTICLE{TRUM94,
  author = {Trumpower, B. L. and Gennis, R. B.},
  title = {Energy Transduction by Cytochrome Complexes in Mitochondrial and
	Bactrerial Respiration: The Enzymology of Coupling Electron Transfer
	Reactions to Transmembrane Proton Translocation},
  journal = ARB,
  year = {1994},
  volume = {63},
  pages = {675},
  note = {Contains statement about mutations of Tyr disabling enzyme.},
  keywords = {Cytochrome c Oxidase}
}

@ARTICLE{VARS94,
  author = {A. Varshney and F. P. Brooks and W. V. Wright},
  title = {Linearly Scalable Computation of Smooth Molecular Surfaces},
  journal = {IEEE Comp.\ Graphics and Applications},
  year = {1994},
  volume = {14},
  pages = {19--25}
}

@ARTICLE{VDAL94,
  author = {M. Viswanathan and P. Droupadi and J. M. Anchin and D. S. Linthicum
	and S. Subramaniam},
  title = {Modeling of the Combining Site of an Antisweet Taste Ligand Antibody},
  journal = {Bioph.\ J.},
  year = {1994},
  volume = {66},
  pages = {a389}
}

@ARTICLE{VOGE94,
  author = {D. Voges and R. Berendes and A. Burger and P. Demange and W. Baumeister
	and R. Huber},
  title = {Three-dimensional structure of membrane-bound annexin {V}--a correlative
	electron microscopy-X-ray crystallography},
  journal = JMB,
  year = {1994},
  volume = {238},
  pages = {199--213},
  number = {2}
}

@ARTICLE{VOLO94,
  author = {A. V. Vologodskii and N. R. Cozzarelli},
  title = {Conformational and thermodynamic properties of supercoiled {DNA}},
  journal = ARBBS,
  year = {1994},
  volume = {23},
  pages = {609--643}
}

@ARTICLE{HIPP94,
  author = {P. H. {Von Hippel}},
  title = {Protein--{DNA} recognition: {N}ew perspectives and underlying themes},
  journal = SCI,
  year = {1994},
  volume = {263},
  pages = {769--770}
}

@ARTICLE{WLDM94,
  author = {Rebecca C. Wade and Brock A. Luty and Eugene Demchuk and Jeffrey
	D. Madura and Malcolm E. Davis and James M. Briggs and J. Andrew
	McCammon},
  title = {Simulation of Enzyme--Substrate Encounter with Gated Active Sites},
  journal = {Structural Biology},
  year = {1994},
  volume = {1},
  pages = {65--69},
  number = {1}
}

@ARTICLE{WAKA94,
  author = {Katsuzo Wakabayashi and Yasunobu Sugimoto and Hidehiro Tanaka and
	Yutaka Ueno and Yasunori Takezawa and Yoshiyuki Amemiya},
  title = {{X}-ray Diffraction Evidence for the Extensibility of Actin and Myosin
	Filaments during Muscle Contraction},
  journal = BJ,
  year = {1994},
  volume = {67},
  pages = {2422--2435}
}

@ARTICLE{WALL94,
  author = {K. R. Wallace and Klaus Schulten},
  title = {A Model of Cortical Processing During Motor Learning},
  journal = BC,
  year = {1994},
  note = {Under revision. [Beckman Institute Technical Report TB-94-11].},
  annote = {Ken likes his citation to read 'K. R. Wallace' and not 'Ken'},
  tbtechrep = {TB-94-11}
}

@ARTICLE{Wang94,
  author = { Wang, D.},
  title = {Some aspects of {H}amiltonian systems and symplectic algorithms},
  journal = {PHYSICA D},
  year = {1994},
  volume = {73},
  pages = { 1--16},
  number = {Nos.~1 and 2},
  nremark = {Nonlinear Phenomena}
}

@BOOK{WARD94,
  title = {The {Radiance} Lighting Simulation and Rendering System},
  publisher = {Computer Graphics},
  year = {1994},
  author = {G. Ward},
  address = {Orlando}
}

@ARTICLE{WARR94,
  author = {N.~Warriar and N.~Pag\'e and M.~V.~Govindan},
  title = {Transcription Activation of Mouse Mammary Tumor Virus--Chloramphenicol
	Acetyltransferase: A Model To Study the Metabolism of Cortisol},
  journal = BCH,
  year = {1994},
  volume = {33},
  pages = {12837--12843},
  number = {43}
}

@ARTICLE{WEIN94A,
  author = {P. Weindler},
  title = {Wintergoldh\"{a}hnchen {\em Regulus regulus} benutzen einen {I}nklinationscompa\ss},
  journal = {J.~Ornithol.},
  year = {1994},
  volume = {135},
  pages = {620--622}
}

@INPROCEEDINGS{WHIT94,
  author = {S. H. White},
  title = {Hydropathy plots and the prediction of membrane protein topology},
  booktitle = {Membrane Protein Structure: Experimental Approaches},
  year = {1994},
  editor = {S. H. White},
  address = {New York},
  publisher = {Oxford University press}
}

@TECHREPORT{WIEG94,
  author = {Wim Wiegerinck and Andrzej Komoda and Tom Heskes},
  title = {Stochastics Dynamics of Learning with Momentum in Neural Networks},
  institution = {University of Illinois},
  year = {1994},
  type = {Beckman Institute Technical Report},
  number = {TB-94-04},
  annote = {Submitted to Journal of Physics A},
  tbtechrep = {TB-94-04}
}

@ARTICLE{WIKS94,
  author = {M. Wikstr{\"o}m and A. Bogachev and M. Finel and J. E. Morgan and
	A. Puustinen and M. Raitio and M. Verkhovskaya and M. I. Verkhovsky},
  title = {Mechanism of Proton Translocation by the Respiratory Oxidases - The
	Histidine Cycle.},
  journal = {Biochimica Et Biophysica Acta Bioenergetics},
  year = {1994},
  volume = {1187},
  pages = {106--111},
  number = {2}
}

@ARTICLE{WOLF94,
  author = {A.~P.~Wolffe},
  title = {Nucleosome positioning and modification: chromatin structure that
	potentiate transcription},
  journal = TIBS,
  year = {1994},
  volume = {19},
  pages = {240--244},
  number = {6},
  annote = {relates bending to nucleosome phasing}
}

@ARTICLE{WOLF94A,
  author = {Alan P. Wolffe},
  title = {Architectural transcription factors},
  journal = SCI,
  year = {1994},
  volume = {264},
  pages = {1100--1101}
}

@ARTICLE{HONG94,
  author = {Xing, Hong and Haase, Steven and Shapiro, David J.},
  title = {Antiestrogens activate an estrogen receptor mutant exhibiting enhanced
	binding to the estrogen response element},
  journal = BBRC,
  year = {1994},
  volume = {202},
  pages = {888--895}
}

@ARTICLE{XU94,
  author = {Dong Xu and Klaus Schulten},
  title = {Coupling of Protein Motion to Electron Transfer in a Photosynthetic
	Reaction Center: Investigating the Low Temperature Behaviour in the
	Framework of the Spin-Boson Model},
  journal = CP,
  year = {1994},
  volume = {182},
  pages = {91--117},
  annote = {May 1, 1994 issue. Note the volume is 182(2,3)},
  tbtechrep = {TB-91-16}
}

@ARTICLE{Xue94,
  author = {Guoliang Xue},
  title = {Molecular Conformation on the {CM-5} by Parallel Two-Level Simulated
	Annealing},
  journal = {JOURNAL OF GLOBAL OPTIMIZATION},
  year = {1994},
  volume = {4},
  pages = {187--208},
  number = {2},
  nremark = {Special issue: Advances in Computational Chemistry and Protein Folding
	co-editors: Panos M. Pardalos, and Guoliang Xue.},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{Yaku94,
  author = {L. V. Yakushevich},
  title = {Nonlinear DNA dynamics: hierarchy of the models},
  journal = {Physica D},
  year = {1994},
  volume = {79},
  pages = {77--86},
  number = {1}
}

@ARTICLE{YAU94,
  author = {J.~L.~W.~Yau and P.~A.~T.~Kelly and J.~R.~Seckl},
  title = {Increased glucocorticoid receptor gene expression in the rat hippocampus
	following combined serotonergic and medical septal cholinergic lesions},
  journal = {Molec. Brain Res.},
  year = {1994},
  volume = {27},
  pages = {174--178},
  annote = {KW: GR, MR, gene expression, aging, hippocampus, in situ hybridization,
	alzheimers}
}

@ARTICLE{YoYa94,
  author = {D. York and W. T. Yang},
  title = {The fast {F}ourier--{P}oisson method for calculating {E}wald sums},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {101},
  pages = {3298--3300}
}

@TECHREPORT{ZhSc94,
  author = {Feng Zhou and Klaus Schulten},
  title = {Long-range force molecular dynamics study on electrostatic and other
	properties of a membrance-water interface},
  institution = {{U}niversity of {I}llinois at {U}rbana-{C}hampaign},
  year = {1994},
  number = {UIUC-BI-TB-94-01}
}

@MISC{BORN93,
  author = {N. Borenstein and N. Freed (Bellcore and Innosoft)},
  title = {{MIME (Multipurpose Internet Mail Extensions) Part One: Mechanisms
	for Specifying and Describing the Format of Internet Message Bodies}},
  month = SEP,
  year = {1993}
}

@INPROCEEDINGS{kale:charm,
  author = {L. V. Kale and S. Krishnan},
  title = {CHARM++ : A Portable Concurrent Object Oriented System Based on {C\texttt{++}}},
  booktitle = {Proceedings of OOPSLA-93},
  year = {1993},
  address = {Washington, DC},
  month = SEP
}

@UNPUBLISHED{GiTa93,
  author = {Roscoe Giles and Pablo Tamayo},
  title = {A Parallel Scalable Approach to Short-Range Molecular Dynamics on
	the {CM}-5},
  month = {April 17},
  year = {1993},
  nremark = {from Ben}
}

@PHDTHESIS{Agar93,
  author = {Pankaj Agarwal},
  title = {Cell-based Computer Models in Developmental Biology},
  school = {New York University},
  year = {1993}
}

@ARTICLE{ARGE93,
  author = {P. Agre and G.M. Preston and B.L. Smith and J.S. Jung and S. Raina
	and C. Moon and W.B. Guggino and S. Nielsen},
  title = {Aquaporin {CHIP} - the Archetypal Molecular Water Channel},
  journal = AJOP,
  year = {1993},
  volume = {265},
  pages = {F463--F476}
}

@ARTICLE{AKEK93,
  author = {Jeung Sun Ahn and Yasuo Kanematsu and Makoto Enomoto and Takashi
	Kushida},
  title = {Determination of Weighted Density States of Vibrational Modes in
	{Zn}-substituted Myoglobin},
  journal = CPL,
  year = {1993},
  volume = {215},
  pages = {336--340}
}

@ARTICLE{AlBS93,
  author = {H. E. Alper and D. Bassolino and T. R. Stouch},
  title = {{C}omputer simulation of a phospholipid monolayer-water system {T}he
	influence of long range forces on water structure and dynamics},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {98},
  pages = {9798}
}

@ARTICLE{ALPE93,
  author = {H. E. Alper and D. Bassolino and T. R. Stouch},
  title = {The limiting behavior of water hydrating a phospholipid monolayer:
	a computer simulation study},
  journal = JCS,
  year = {1993},
  volume = {99},
  pages = {5547}
}

@ARTICLE{ALPE93A,
  author = {H. E. Alper and D. Bassolino and T. R. Stouch},
  title = {Computer simulation of a phospholipid monolayer-water system: {The}
	influence of long range forces on water structure and dynamics},
  journal = JCS,
  year = {1993},
  volume = {98},
  pages = {9798},
  annote = {long range coulomb interaction has important effect on water in a
	membrane-water interface. Water layer up to 60-90 {\AA\ } simulated,
	and cutoff up to 30 {\AA\ } used. DMPC lipid from previous simulation,
	all atom model. 320 K, 1fs step. periodic boundary. Water coordination
	number and average movement per 100fs used in analysis.}
}

@ARTICLE{ALPE93B,
  author = {H. E. Alper and D. Bassolino and T. R. Stouch},
  title = {The limiting behavior of water hydrating a phospholipid monolayer:
	a computer simulation study},
  journal = JCS,
  year = {1993},
  volume = {99},
  pages = {5547}
}

@ARTICLE{AMAD93,
  author = {A. Amadei and A.~B.~M. Linnsen and H.~J.~C. Berendsen},
  title = {Essential Dynamics of Proteins},
  journal = PSFG,
  year = {1993},
  volume = {17},
  pages = {412--425}
}

@ARTICLE{AQVI93,
  author = {J. Aquist and A. Warshel},
  title = {Simulation of Enzyme Reactions Using Valence Bond Force Fields and
	Other Hybrid Quantum/Classical Approaches},
  journal = CR,
  year = {1993},
  volume = {93},
  pages = {2523--2544}
}

@ARTICLE{BALA93,
  author = {S. P. Balashov and R. Govindjee and M. Kono and E. Imasheva and E.
	Lukashev and T. G. Ebrey and R. K. Crouch and D. R. Menick and Y.
	Feng},
  title = {Effect of the Arginine-82 to Alanine Mutation in Bacteriorhodopsin
	on Dark Adaptation, Proton Release, and the Photochemical Cycle},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {10331--10343}
}

@ARTICLE{BASS93,
  author = {D. Bassolino and H. E. Alper and T. R. Stouch},
  title = {Solute Diffusion in Lipid Bilayer Membranes: An atomic level study
	by molecular dynamics simulations},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {12624}
}

@ARTICLE{BATC93,
  author = {S. Batchelor and C.W.M. Kay and K.A. McLaughlan and I.A. Shkrob},
  title = {Time-resolved and modulation methods in the study of the effects
	of magnetic fields on the yields of free radical reactions},
  journal = {J.~Phys.~Chem.},
  year = {1993},
  volume = {97},
  pages = {13250--13258}
}

@ARTICLE{BAYB93,
  author = {T. Bayburt and B.-Z. Yu and H.-K. Lin and J. Browning and M. K. Jain
	and M.H. Gelb},
  title = {Human nonpancreatic secreted phospholipase {A$_2$}: Interfacial parameters,
	substrate specificities, and competitive inhibitors},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {573--582}
}

@ARTICLE{BECK93,
  author = {O. M. Becker and M. Karplus},
  title = {Temperature Echoes in Molecular Dynamics Simulations of Proteins},
  journal = PRL,
  year = {1993},
  volume = {70},
  pages = {3514--3517},
  number = {22}
}

@ARTICLE{BERC93,
  author = {H. Berchtold and L. Reshetnikova and C. O. Reiser and N. K. Schirmer
	and M. Sprinzl and R. Hilgenfeld},
  title = {Crystal structure of active elongation factor {Tu} reveals major
	domain rearrangements},
  journal = NAT,
  year = {1993},
  volume = {365},
  pages = {126--132}
}

@ARTICLE{BERE93,
  author = {H. Berendsen and J. Mavri},
  title = {Quantum Simulation of Reaction Dynamics by Density Matrix Evolution},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {13464--13468}
}

@ARTICLE{BeMa93,
  author = {H. J. C. Berendsen and J. Mavri},
  title = {Quantum Simulation of Reaction Dynamics by Density Matrix Evolution},
  journal = {J. Phys. Chem.},
  year = {1993},
  volume = {97},
  pages = {13464--13468}
}

@UNPUBLISHED{Bies93,
  author = {J. Biesiadecki},
  title = {Dangers of Using Multiple Time Step Algorithms for Molecular Dynamics
	Simulations},
  note = {M.S. thesis},
  year = {1993},
  institution = {Dept.\ Computer Sci., Univ.\ Illinois}
}

@ARTICLE{BiSk93,
  author = {J.~J. Biesiadecki and R.~D. Skeel},
  title = {Dangers of Multiple-Time-Step Methods},
  journal = {J. Comput. Phys.},
  year = {1993},
  volume = {109},
  pages = {318--328},
  number = {2},
  nack = {NSF90, NIH92},
  nremark = {symplectic MTS(Verlet I) and Verlet X}
}

@ARTICLE{BOYE93,
  author = {Paul D. Boyer},
  title = {The binding change mechanism for ATP synthase--some probabilities
	and possibilities},
  journal = BBA,
  year = {1993},
  volume = {1140},
  pages = {215--250}
}

@ARTICLE{BPCR93,
  author = {A. Brass and B. J. Pendleton and Y. Chen and B. Robson},
  title = {Hybrid {M}onte {C}arlo Simulations Theory and Initial Comparison
	with Molecular Dynamics},
  journal = {Biopolymers},
  year = {1993},
  volume = {33},
  pages = {1307--1315}
}

@ARTICLE{BrCa93,
  author = {Charles L. Brooks and David A. Case},
  title = {Simulations of Peptide Conformation Dynamics and Thermodynamics},
  journal = {Chem. Rev.},
  year = {1993},
  volume = {93},
  pages = {2487--2502}
}

@ARTICLE{BROW93,
  author = {L. S. Brown and L. Zimanyi and R. Needleman and M. Ottolenghi and
	J. K. Lanyi},
  title = {PHOTOREACTION OF THE {N}-INTERMEDIATE OF BACTERIORHODOPSIN, AND ITS
	RELATIONSHIP TO THE DECAY KINETICS OF THE {M}-INTERMEDIATE.},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {7679--7685}
}

@ARTICLE{BROW93A,
  author = {S. J. Brown and P. J. Kellett and S. J. Lippard},
  title = {Ixr1, a yeast protein that binds to platinated {DNA} and confers
	sensitivity to cisplatin},
  journal = SCI,
  year = {1993},
  volume = {261},
  pages = {603--605}
}

@ARTICLE{BrKi93,
  author = {Douglas Brune and Sangtae Kim},
  title = {Predicting Protein Diffusion Coefficients},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1993},
  volume = {90},
  pages = {3835--3839}
}

@ARTICLE{BrME93,
  author = {J.-P. Brunet and J.P. Mesirov and A. Edelman},
  title = {Hypercube algorithms for direct N-body solvers of different granularities},
  journal = SJSC,
  year = {1993},
  volume = {14},
  pages = {1143--1158}
}

@ARTICLE{BuCM93,
  author = {C.~E. Bugg and W.~M. Carson and J.~A. Montgomery},
  title = {Drugs by Design},
  journal = SA,
  year = {1993},
  pages = {92--98}
}

@ARTICLE{BURA93,
  author = {W.R. Burack and Q. Yuan and R.L. Biltonen},
  title = {Role of lateral phase separation in the modulation of phospholipase
	{A$_2$} activity},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {583--589},
  annote = {phase transition}
}

@ARTICLE{CaSa93,
  author = {M.P. Calvo and J.M. Sanz-Serna},
  title = {The development of variable-step symplectic integrators, with applications
	to the two-body problem},
  journal = SJSSC,
  year = {1993},
  volume = {14},
  pages = {936--952}
}

@ARTICLE{Case93,
  author = {D.A. Case},
  title = {Computer Simulations of Protein Dynamics and Thermodynamics},
  journal = {Computer},
  year = {1993},
  pages = {59--67},
  nremark = {good for telling what one should compute}
}

@ARTICLE{CHAN93,
  author = {A. Chan and E. Hutchinson and D. Harris and J. Thornton},
  title = {Identification, classification, and analysis of beta-bulges in proteins.},
  journal = PS,
  year = {1993},
  volume = {2},
  pages = {1574--1590}
}

@ARTICLE{CHEN93,
  author = {Xin Chen and R. Kimberley Cook and Peter A. Rubenstein},
  title = {Yeast Actin with a Mutation in the ``Hydrophobic Plug'' between Subdomains
	3 and 4 ({L$_{266}$D}) Displays a Cold-sensitive Polymerization Defect},
  journal = JCB,
  year = {1993},
  volume = {123},
  pages = {1185--1195}
}

@ARTICLE{CLAR93,
  author = {P. A. Clark and J. N. Jansonius and E. L. Mehler},
  title = {Semiempirical Calculations of the Electronic Absorption Spectra of
	Vitamin-{B6} Derivatives in the Active Site of Mitochondrial Aspartate
	Aminotranferase},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {1894--1902}
}

@ARTICLE{CLOR93,
  author = {G. M. Clore and A. Bax and M. Ikura and A. M. Gronenborn},
  title = {Structure of calmodulin-target peptide complexes},
  journal = COSB,
  year = {1993},
  volume = {3},
  pages = {838--845}
}

@INPROCEEDINGS{COGD93,
  author = {R.J. Cogdell and A.M. Hawthornthwaite},
  title = {Preparation, Purification, and Crystallization of Purple Bacteria
	Antenna Complexes},
  booktitle = {The Photosynthetic Reaction Center},
  year = {1993},
  editor = {J. Deisenhofer and J.R. Norris},
  pages = {23},
  address = {San Diego},
  publisher = {Academic Press}
}

@ARTICLE{COLE93,
  author = {B.~D. Coleman and E.~H. Dill and M. Lembo and Z. Lu and I. Tobias},
  title = {On the dynamics of rods in the theory of {Kirchhoff and Clebsch}},
  journal = {Arch.\ Rational Mech.\ Anal.},
  year = {1993},
  volume = {121},
  pages = {339--359},
  publisher = {Springer-Verlag}
}

@BOOK{CREI93,
  title = {Proteins},
  publisher = {W. H. Freeman and Company},
  year = {1993},
  author = {T. E. Creighton},
  address = {New York},
  edition = {2nd}
}

@ARTICLE{CROT93,
  author = {D.~M.~Crothers},
  title = {Architectural elements in nucleoprotein complexes},
  journal = CB,
  year = {1993},
  volume = {3},
  pages = {675--676},
  number = {10}
}

@INPROCEEDINGS{CRUZ93,
  author = {Carolina Cruz-Neira and Dan J. Sandin and Thomas A. DeFanti},
  title = {Surround-Screen Projection-Based Virtual Reality: The Design and
	Implementation of the {CAVE}},
  booktitle = {Proceedings of SIGGRAPH '93},
  year = {1993},
  pages = {135--142},
  address = {Anaheim, CA},
  publisher = {Association for Computing Machinery}
}

@ARTICLE{DaLe93,
  author = {V. Dagget and M. Levitt},
  title = {Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations},
  journal = {J. Mol. Biol.},
  year = {1993},
  volume = {232},
  pages = {600--618}
}

@ARTICLE{DAGG93,
  author = {V. Daggett and M. Levitt},
  title = {Realistic simulations of native-protein dynamics in solution and
	beyond},
  journal = ARBBS,
  year = {1993},
  volume = {22},
  pages = {353--380}
}

@ARTICLE{DAMO93,
  author = {K.V. Damodaran and K.M. {Jr. Merz}},
  title = {Head Group--water interactions in lipid bilayers: a comparison between
	DMPC- and DLPE-based lipid bilayers},
  journal = {Langmuir},
  year = {1993},
  volume = {9},
  pages = {1179--1183}
}

@ARTICLE{DaYP93,
  author = {T. Darden and D. York and L. Pedersen},
  title = {Particle mesh {E}wald: An {N} log({N}) method for {E}wald sums in
	large systems},
  journal = JCP,
  year = {1993},
  volume = {98},
  pages = {10089--10092},
  number = {12},
  annote = {An N - log(N) method for evaluating electrostatic energies and forces
	of large periodic systems is presented. The method is based on interpolation
	of the reciprocal space Ewald sums and evaluation of the resulting
	convolutions using fast Fourier transforms. Timings and accuracies
	are presented for three large crystalline ionic systems.}
}

@ARTICLE{DeKo93,
  author = {Stephen E. DeBolt and Peter A. Kollman},
  title = {{AMBERCUBE MD}, Parallelization of {AMBER}'s Molecular Dynamics Module
	for Distributed-Memory Hypercube Computers},
  journal = {J. Comput.\ Chem},
  year = {1993},
  volume = {14},
  pages = {312--329},
  number = {3}
}

@ARTICLE{DELL93,
  author = {M. J. Dellwo and A. J. Wand},
  title = {The Influence of Methyl Rotor Dynamics on Hydrogen Relaxation Networks:
	Derivation of Spectral Densities in Model Free Form},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {1886--1893}
}

@ARTICLE{DELL93A,
  author = {M. J. Dellwo and A. J. Wand},
  title = {Computationally Efficient Distance-Based Gradients for the Refinement
	of Structure Using Rate Matrix Analyses},
  journal = JBNMR,
  year = {1993},
  volume = {3},
  pages = {205--214}
}

@ARTICLE{DEMC93,
  author = {A. P. Demchenko},
  title = {Dielectric Behaviour of Proteins},
  journal = JML,
  year = {1993},
  volume = {56},
  pages = {127--139}
}

@ARTICLE{DIST93,
  author = {C.~W.~Distelhorst},
  title = {Steroid hormone receptors},
  journal = {J.\ Lab.\ Clin.\ Med.},
  year = {1993},
  volume = {122},
  pages = {241--244},
  annote = {review of steroid hormones, see also FREE92}
}

@ARTICLE{DOLA93,
  author = {C. Dolainsky and A. Mops and T. M. Bayerl},
  title = {Transverse Relaxation in Supported and Nonsupported Phospholipid
	Model Membranes and the Influence of Ultraslow Motions --- A {P-31-{NMR}}
	Study},
  journal = JCP,
  year = {1993},
  volume = {98},
  pages = {1712--1720},
  number = {2},
  abstract = {The effect of motions which are slow on the {NMR} time scale (in particular,
	lateral diffusion) on the P-31-{NMR} transverse relaxation behavior
	of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) phospholipid
	membranes was studied by experiment and computer simulation. Two
	new membrane model systems (spherical supported vesicles) which exhibit
	some unique geometrical features and physical properties as well
	as the commonly used multilamellar vesicles, were applied for the
	measurement of the P-31-{NMR} anisotropic transverse relaxation times.
	The known geometry of the new membrane model systems under study
	enables a direct comparison of the experimental transverse relaxation
	spectra with those obtained by a spectral simulation technique which
	considers random diffusion on the surface of a sphere as the dominant
	relaxation mechanism, where the sphere size corresponds to that used
	in the experiments. The transverse relaxation times obtained experimentally
	for the three model systems studied differ drastically, where the
	multilamellar vesicles exhibit the longest T2 and single spherical
	supported bilayers show the shortest relaxation time. Both experiment
	and simulation indicate that lateral diffusion causes anisotropic
	transverse relaxation which scales with the angle theta between molecular
	director axis and magnetic field as I/T2 approximately Sin2theta
	Cos2theta. An analysis of the experimental data obtained for supported
	systems suggests that diffusion of the individual molecules along
	the surface of the sphere is superimposed by diffusion over an "adiabatic
	rough" surface (a "quasistationary " roughness on the time scale
	of the echo experiment). This provides a significant additional contribution
	to the transverse relaxation time T2. A comparison of single bilayers
	and multibilayers on a solid support, respectively, indicates that
	this roughness is mainly a property of the single supported bilayers,
	most likely due to an area mismatch between the bilayer and the surface
	of its solid support.},
  address = {tech univ munich,dept phys e22, w-8046 garching, germany.},
  annote = {requested Tx=19930216.},
  keywords = {magnetic-resonance. bilayer-membranes. spin-relaxation. lipid-bilayers.
	spectra.}
}

@ARTICLE{DONN93,
  author = {D. Donnelly and J. P. Overington and S. V. Ruffle and J. H. Nugent
	and T . L. Blundell},
  title = {Modeling $\alpha$-helical transmembrane domains: the calculation
	and use of substitution tables for lipid-facing residues},
  journal = {Protein Science},
  year = {1993},
  volume = {2},
  pages = {55}
}

@ARTICLE{DRAC93,
  author = {L. A. Drachev and S. V. Dracheva and A. D. Kaulen},
  title = {{pH} dependence of the formation of an {M}-type intermediate in the
	photocycle of 13-{\it cis}-bacteriorhodopsin.},
  journal = FEBS,
  year = {1993},
  volume = {332},
  pages = {67--70}
}

@ARTICLE{DU93,
  author = {M. Du and G. Fleming},
  title = {Femtosecond Time-Resolved Fluorescence Spectroscopy of Bacteriorhodopsin:
	Direct Observation of Excited State Dynamics in the Primary Step
	of the Proton Pump Cycle},
  journal = BC,
  year = {1993},
  volume = {48},
  pages = {101--111}
}

@INCOLLECTION{EBRE93,
  author = {T. Ebrey},
  title = {Light Energy Transduction in Bacteriorhodopsin},
  booktitle = {Thermodynamics of Membranes, Receptors and Channels},
  publisher = {{CRC} Press},
  year = {1993},
  editor = {M. Jacobson},
  pages = {353--387},
  address = {New York}
}

@ARTICLE{EISE93,
  author = {F. Eisenmenger and P. Argos and R. Abagyan},
  title = {A method to configure protein side-chains from the main-chain trace
	in homology modelling},
  journal = JMB,
  year = {1993},
  volume = {231},
  pages = {849--860}
}

@ARTICLE{EISF93,
  author = {W. Eisfeld and C. Pusch and R. Diller and R. Lohrmann and M. Stockburger},
  title = {Resonance {Raman} and Optical Transient Studies of the Light-Induced
	Proton Pump of Bacteriorhodopsin Reveal Parallel Photocycles},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {7196--7215}
}

@ARTICLE{ERIC93,
  author = {H. P. Erickson},
  title = {Tenascin-{C}, tenascin-{R} and tenascin-X: a family of talented proteins
	in search of functions},
  journal = COCB,
  year = {1993},
  volume = {5},
  pages = {869--876}
}

@ARTICLE{EBHN93,
  author = {M.~A.~L.~Eriksson and H.~Berglund and T.~H{\"a}rd and L.~Nilsson},
  title = {A comparison of $^{15}$N {NMR} relaxation Measurements with a molecular
	dynamics simulation: backbone dynamics of the Glucocorticoid receptor
	{DNA}--binding domain.},
  journal = PSFG,
  year = {1993},
  volume = {17},
  pages = {375--390}
}

@INCOLLECTION{ERWI93,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {A Comparison of Models of Visual Cortical Map Formation},
  booktitle = {Computation and Neural Systems},
  publisher = {Kluwer Academic Publishers},
  year = {1993},
  editor = {Frank H. Eeckman and James M. Bower},
  chapter = {60},
  pages = {395--402},
  tbtechrep = {TB-92-16}
}

@ARTICLE{ESPO93,
  author = {M. Degli Esposti and S. De Vries and M. Crimi and A. Ghelli and T.
	Patarnello and A. Meyer},
  title = {Mitochondrial cytochrome $b$: evolution and structure of the protein},
  journal = BBA,
  year = {1993},
  volume = {1143},
  pages = {243--271}
}

@ARTICLE{EVAN93,
  author = {S. V. Evans},
  title = {{SETOR}: Hardware Lighted Three-Dimensional Solid Model Representations
	of Macromolecules},
  journal = JMG,
  year = {1993},
  volume = {11},
  pages = {134--138}
}

@ARTICLE{FALS93,
  author = {S.~ Falsafi and N.~O.~Reich},
  title = {Molecular Dynamics Simulations of {B-DNA}: An Analysis of the role
	of Initial Molecular Configuration, Randomly Assigned Velocity Distribution,
	Long Integration Times, and Nonconstr ained Termini},
  journal = BP,
  year = {1993},
  volume = {33},
  pages = {459--473},
  annote = {amber3.0 implicit solvent, distance dependent dielectric, solvated
	counterions, dodecamer d({CGCGAATTCGC}), 89\ps\, no harmonics, end
	effects did not extend beyond 2 end bps, stabilizes with/in 100-200ps}
}

@ARTICLE{FATT93,
  author = {D.R. Fattal and A. Ben-Shaul},
  title = {A molecular model for lipid--protein interaction in membranes: the
	role of hydrophobic mismatch},
  journal = BJ,
  year = {1993},
  volume = {65},
  pages = {1795--1809}
}

@ARTICLE{FERE93,
  author = {A. E. Ferentz and T. A. Keating and G. L. Verdine},
  title = {Synthesis and characterization of disulfide cross-linked oligonucleotides},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {9006--9014}
}

@ARTICLE{FERR93,
  author = {M. Ferrand and G. Zacca{\"{\i}} and M. Nina and J.C. Smith and C.
	Etchesbest and B. Roux},
  title = {Structure and dynamics of bacteriorhodopsin - Comparison of simulation
	and experiment},
  journal = FEBS,
  year = {1993},
  volume = {327},
  pages = {256--260}
}

@INPROCEEDINGS{FRAN93C,
  author = {H.A. Frank},
  title = {Carotenoids in photosynthetic bacterial reaction centers: structure,
	spectroscopy, and photochemistry},
  booktitle = {The photosynthetic reaction center},
  year = {1993},
  volume = {2},
  pages = {221--237},
  publisher = {Academic Press}
}

@ARTICLE{FRAN93B,
  author = {H.A. Frank and V Chynwat and G . Hartwich and M. Meyer and I. Katheder
	and H. Scheer},
  title = {Carotenoid triplet state formation in {\em Rhodobacter sphaeroides}
	R-26 reaction centers exchanged with modified bacteriochlorophyll
	pigments and reconstituted with spheroidene},
  journal = {Photosyn.~Res.},
  year = {1993},
  volume = {37},
  pages = {193--203}
}

@ARTICLE{FRAN93A,
  author = {H.A. Frank and R. Farshoosh and M.L. Aldema and B. DeCoster and R.L.
	Christensen and R. Gebhard and J. Lugtenburg},
  title = {Carotenoid-toBacteriochlorophyll singlet energy transfer in carotenoid-incorporated
	{B}850 light-harvesting complexes of {\em {R}hodobacter sphaeroides}
	{R}-26.1},
  journal = {Photochem.~Photobiol.~},
  year = {1993},
  volume = {57},
  pages = {49--55}
}

@ARTICLE{FREE93,
  author = {L.~P.~Freedman and B.~F.~Luisi},
  title = {On the mechanism of {DNA} binding by nuclear hormone receptors: a
	structural and functional perspective.},
  journal = JCBC,
  year = {1993},
  volume = {51},
  pages = {140--150}
}

@ARTICLE{LUIS93,
  author = {Leonard P. Freedman and Ben F. Luisi},
  title = {On the Mechanism of {DNA} Binding by Nuclear Hormone Receptors: A
	Structural and Functional Perpective},
  journal = {Journal of Cellular Biochemistry},
  year = {1993},
  volume = {51},
  pages = {140--150}
}

@ARTICLE{GARD93,
  author = {A.T. Gardiner and R.J. Cogdell and S. Takaichi},
  title = {The effect of growth conditions on the light-harvesting apparatus
	in {\em {R}hodopseudomonas acidophila}},
  journal = {Photosyn.~Res.},
  year = {1993},
  volume = {38},
  pages = {159--168}
}

@ARTICLE{GAT93,
  author = {Y. Gat and M. Sheves},
  title = {A Mechanism for Controlling the {pK}$_{{\rm a}}$ of the Retinal Protonated
	{Schiff} Base in Retinal Proteins. \ {A} Study With Model Compounds},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {3772--3773}
}

@ARTICLE{GENN93,
  author = {R. B. Gennis and B. Barquera and B. Hacker and S. R. Van~Doren and
	S. Arnaud and A. R. Crofts and E. Davidson and K. A. Gray and F.
	Daldal},
  title = {The $bc_1$ complexes of {{\em {R}hodobacter sphaeroides}} and {{\em
	{R}hodobacter capsulatus}}},
  journal = JBB,
  year = {1993},
  volume = {25},
  pages = {195--209}
}

@ARTICLE{GER93,
  author = {L. Germeroth and F. Lottspeich and B. Robert and H. Michel},
  title = {Unexpected similarities of the {B}800-850 light-harvesting complex
	from {{\it {R}hodospirillum molischianum\/}} to the {B}870 light-harvesting
	complexes from other purple photosynthetic bacteria},
  journal = {Biochemistry},
  year = {1993},
  volume = {32},
  pages = {5615--5621}
}

@ARTICLE{GERM93,
  author = {L. Germeroth and F. Lottspeich and B. Robert and H. Michel},
  title = {Unexpected Similarities of the {B}800-850 Light-Harvesting Complex
	from {{\it {R}hodospirillum molischianum\/}} to the {B}870 Light-Harvesting
	Complexes from Other Purple Photosynthetic Bacteria},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {5615--5621}
}

@ARTICLE{GERS93,
  author = {Mark Gerstein and Bryan F. Anderson and Gillian E. Norris and Edward
	N. Baker and Arthur M. Lesk and Cyrus Chothia},
  title = {Domain Closure in Lactoferrin},
  journal = JMB,
  year = {1993},
  volume = {234},
  pages = {357--372}
}

@ARTICLE{GILL93,
  author = {T. Gillbro and P. O. Andersson and R. S. H. Liu, A. E. Asato and
	S. Takaishi and R. J. Cogdell},
  title = {Location of the carotenoid 2A$_g$-state and its role in photosynthesis},
  journal = PCPB,
  year = {1993},
  volume = {57},
  pages = {44--48}
}

@ARTICLE{GITT93,
  author = {Frederick Gittes and Brian Mickey and Jilda Nettleton and Jonathon
	Howard},
  title = {Flexural Rigidity of Microtubules and Actin Filaments Measured from
	Thermal Fluctuations in Shape},
  journal = JCB,
  year = {1993},
  volume = {120},
  pages = {923--934}
}

@ARTICLE{GlGr93,
  author = {J. A. Glazier and F. Graner},
  title = {Simulation of the Differential Adhesion Driven Rearrangement of Biological
	Cells},
  journal = PRE,
  year = {1993},
  volume = {47},
  pages = {2128--2154},
  number = {3}
}

@ARTICLE{GOOD93,
  author = {C.~Goodman and C.~Shatz},
  title = {Developmental mechanisms that generate precise patterns of neuronal
	connectivity},
  journal = {Cell},
  year = {1993},
  volume = {72},
  pages = {77--89}
}

@ARTICLE{GORS93,
  author = {Jack Gorski and Furlow, J. David and Murdoch, Fern E. and Fritsch,
	Michael and Kaneko, Kotaro and Ying, Ghingwen and Malayer, Jerry
	R.},
  title = {Perturbations in the Model of Estrogen Receptor Regulation of Gene
	Expression},
  journal = {Biology of Reproduction},
  year = {1993},
  volume = {48},
  pages = {8--14}
}

@ARTICLE{GREE93,
  author = {Duncan A. Greenhalgh and David L Farrens and Sriram Subramaniam and
	H. Gobind Khorana},
  title = {Hydrophobic Amino Acids in the Retinal-binding Pocket of Bacteriorhodopsin},
  journal = JBC,
  year = {1993},
  volume = {268},
  pages = {20305--20311}
}

@ARTICLE{HACK93,
  author = {B. Hacker and B. Barquera and A. R. Crofts and R. B. Gennis},
  title = {Characterization of mutations in the cytochrome $b$ subunit of the
	$bc_1$ complex of {{\em {R}hodobacter sphaeroides}} that affect the
	quinone reductase site ({Q}${}_c$)},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {4403--4410}
}

@BOOK{HaNW93,
  title = {Solving Ordinary Differential Equations I: \mbox{N}on-stiff Systems},
  publisher = {Springer-Verlag},
  year = {1993},
  author = {Ernst Hairer and S. P. N{\o}{r}sett and G. Wanner},
  address = {Berlin},
  edition = {2nd},
  nremark = {Call Number: QA372.H16}
}

@ARTICLE{Hans93,
  author = {J.-P. Hansen},
  title = {The kinetic glass transition: what can we learn from molecular dynamics
	simulations?},
  journal = {PHYSICA A (Statistical and Theoretical Physics)},
  year = {1993},
  volume = {201},
  pages = {138},
  number = {Nos.~1, 2 and 3},
  nremark = {Proceedings of the International Workshop on Dynamics of Disordered
	Materials II, Grenoble, France, CHAPTER 4. COMPUTER SIMULATION,}
}

@ARTICLE{HELL93,
  author = {Helmut Heller and Michael Schaefer and Klaus Schulten},
  title = {Molecular Dynamics Simulation of a Bilayer of 200 Lipids in the Gel
	and in the Liquid Crystal-Phases},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {8343--8360},
  annote = {Previous title: ``Construction, Molecular Dynamics Simulation and
	Analysis of a Lipid Bilayer''; Coordinates available through Brookhaven
	protein data bank, ID Code 1TOY},
  tbtechrep = {TB-92-18 and TB-93-03}
}

@ARTICLE{HeSS93,
  author = {Helmut Heller and Michael Schaefer and Klaus Schulten},
  title = {Molecular Dynamics Simulation of a Bilayer of 200 Lipids in the Gel
	and in the Liquid Crystal-Phases},
  journal = {J. Phys.\ Chem.},
  year = {1993},
  volume = {97},
  pages = {8343--8360},
  annote = {Previous title: ``Construction, Molecular Dynamics Simulation and
	Analysis of a Lipid Bilayer''; Coordinates available through Brookhaven
	protein data bank, ID Code 1TOY},
  tbtechrep = {TB-92-18 and TB-93-03}
}

@TECHREPORT{HERZ93,
  author = {Andreas V. M. Herz},
  title = {Global Analysis of Recurrent Neural Networks},
  institution = {University of Illinois},
  year = {1993},
  type = {Beckman Institute Technical Report},
  number = {TB-93-12},
  tbtechrep = {TB-93-12}
}

@TECHREPORT{HESK93a,
  author = {Tom Heskes},
  title = {On {F}okker-{P}lank Approximations of On-Line Learning Processes},
  institution = {University of Illinois},
  year = {1993},
  type = {Beckman Institute Technical Report},
  number = {TB-93-14},
  tbtechrep = {TB-93-14}
}

@BOOK{Hilb93,
  title = {Chaos and Nonlinear Dynamics},
  publisher = {Oxford Univ.},
  year = {1993},
  author = {Robert C. Hilborn},
  address = {New York}
}

@ARTICLE{HILD93,
  author = {V. Hildebrandt and K. Fendler and J. Heberle and A. Hoffmann and
	E. Bamberg and G. B{\"u}ldt},
  title = {Bacteriorhodopsin Expressed in {\it Schizosaccharomyces pombe} Pumps
	Protons Through the Plasma Membrane},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {3578--3582}
}

@ARTICLE{HODE93,
  author = {Hodel, A. and Simonson, T. and Fox, R. O. and Br{\"u}nger, A. T.},
  title = {Model Bias in Macromolecular Crystal Structure},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {3409--3417}
}

@ARTICLE{HOLM93,
  author = {Liisa Holm and Chris Sander},
  title = {Structure Comparison by Alignment of Distance Matrices},
  journal = JMB,
  year = {1993},
  volume = {233},
  pages = {123--138}
}

@PHDTHESIS{Hols93,
  author = {M. Holst},
  title = {Multigrid Solution of the {P}oisson--{B}oltzmann Equation},
  school = {Dept.\ of Computer Science, Univ.\ of Illinois at Urbana--Champaign},
  year = {1993},
  nack = {doe}
}

@ARTICLE{HONI93,
  author = {B.~Honig and K.~Sharp and A.~Yang},
  title = {Macroscopic Models of Aqueous Solutions: Biological and Chemical
	Applications},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {1101--1109},
  annote = {theorectical approach to solvent solute interaction using PB eqn}
}

@ARTICLE{HOSL93,
  author = {J. P. Hosler and S. {Ferguson-Miller} and M. W. Calhoun and J. W.
	Thomas and J. Hill and L. Lemieux and J. Ma and C. Georgiou and J.
	Fetter and J. P. Shapleigh and others},
  title = {Insight into the active-site structure and function of cytochrome
	oxidase by analysis of site-directed mutants of bacterial cytochrome
	aa$_3$ and cytochrome bo},
  journal = {J. Bioenerg. Biomembr.},
  year = {1993},
  volume = {25},
  pages = {1210--136}
}

@ARTICLE{WIDO93,
  author = {J. ~Yao, P. T. ~Lowary, J. ~Widom},
  title = {Twist constraints on linker {DNA} in the 30-nm chromatin fiber: Impications
	for nucleosome phasing.},
  journal = {Biochemistry},
  year = {1993},
  volume = {90},
  pages = {9364--9368}
}

@ARTICLE{JAIN93,
  author = {M. K. Jain and B.P. Maliwal},
  title = {Spectroscopic properties of the states of pig pancreatic phospholipase
	{A$_2$} at interfaces and their possible molecular origin},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {11838--11846}
}

@ARTICLE{JAIN93a,
  author = {M. K. Jain and J. Rogers and H.S. Henderickson and O.G. Berg},
  title = {The chemical step is not rate-limiting during the hydrolysis by phospholipase
	{A$_2$} of mixed micelles of phospholipid and detergent},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {8360--8367}
}

@ARTICLE{JAIN93b,
  author = {M. K. Jain and B.Z. Yu and O.G. Berg},
  title = {Relationship of interfacial equilibria to interfacial activation
	of phospholipase {A$_2$}},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {11319--11329},
  annote = {increased intrinsic affinity toward the active-site-directed ligands}
}

@ARTICLE{Jako93,
  author = {Eric Jakobsson},
  title = {Hierarchies of Simulation Methods in Understanding Biomolecular Function},
  journal = {FIXME},
  year = {1993}
}

@ARTICLE{JaOr93,
  author = {D. Jane\v{z}i\v{c} and B. Orel},
  title = {Implicit {R}unge-{K}utta Method for Molecular Dynamics Integration},
  journal = {J. Chem.\ Inf.\ Comput.\ Sci.},
  year = {1993},
  volume = {33},
  pages = {252--257}
}

@TECHREPORT{Jay93,
  author = {Jay, L.},
  title = {Symplectic partitioned {R}unge-{K}utta methods for constrained {H}amiltonian
	systems},
  institution = {Universit\'e de Gen\`eve},
  year = {1993}
}

@ARTICLE{KJDN93,
  author = {Rajiv K. Kalia Wei Jin and Simon W. de Leeuw and Aiichiro Nakano
	and Priya Vashishta},
  title = {Atomistic Simulations on Parallel Architectures},
  journal = {Intl J, Quantum Chem.},
  year = {1993},
  volume = {27},
  pages = {781--792},
  nabstract = {Algorithms are designed to implement molecular-dynamics simulations
	on emerging concurrent architectures. For systems with finite-range
	interactions, a domain decomposition algorithm is used to implement
	the multiple-time-step (MTS) approach to molecular-dynamics (MD)
	simulations on distributed-memory multiple instructions multiple
	data (MIMD) machines. This approach reduces the computation of forces
	significantly by exploiting the different time scales for short-range
	and intermediate-range interactions. Parallel algorithms are also
	designed for MD simulations of bulk Coulombic systems. The performance
	of these algorithms is tested on the Intel iPSC/860 system.The computational
	complexity of these algorithms is O(N) and parallel efficiencies
	close to 0.9. Molecular-dynamics simulations are carried out to investigate
	the structural and dynamical properties of highly densified and also
	porous silica glasses. Changes in the short-range and intermediate-range
	order in amorphous SiO2 are determined at different densities in
	the range of 4.28-0.1 g/cm(3). Results for internal surface area
	and surface-to-volume ratio in porous SiO2 are also discussed. (C)
	1993 John Wiley and Sons, Inc.}
}

@ARTICLE{JoMM93,
  author = {C.R. Johnson and R.S. MacLeod and M.A. Matheson},
  title = {Computational medicine: bioelectric field problems},
  journal = {Computer},
  year = {1993},
  pages = {47--57}
}

@ARTICLE{JORG93,
  author = {K. Jorgensen and M.M. Sperotto and O.G. Mouritsen and J.H. Ipsen
	and M.J. Zukermann},
  title = {Phase equilibria and local structure in binary lipid bilayers},
  journal = BBA,
  year = {1993},
  note = {submitted}
}

@ARTICLE{TOR93,
  author = {L.~Joshua-Tor and J.~.L~Sussman},
  title = {The coming of age of {DNA} crystallography},
  journal = COSB,
  year = {1993},
  volume = {3},
  pages = {323--335},
  annote = {this gives many references to other {DNA}xray structs, also it's
	a good ref to point out number of published DNA structures and that
	emphasis on {DNA}struc is not just better resolution but new conformations
	and co-crystals with drugs. also mentions the nucleic acid database
	NDB men=ntions growth in number of protien structs also}
}

@ARTICLE{JUMI93,
  author = {D. Juminaga and S. A. Albaugh and R. F. Steiner},
  title = {The Interaction of Calmodulin with Regulatory Peptides of Phosphorylase
	Kinase},
  journal = JBC,
  year = {1993},
  volume = {269},
  pages = {1660--1667}
}

@ARTICLE{KATA93,
  author = {M. Kataoka and K. Mihara and H. Kamikubo and R. Needleman and J.
	K. Lanyi},
  title = {Trimeric Mutant Bacteriorhodopsin, {D85N}, Shows A Monophasic {CD}
	Spectrum},
  journal = FEBS,
  year = {1993},
  volume = {333},
  pages = {111--113}
}

@ARTICLE{KeLe93,
  author = {David A.\ Kessler and Herbert Levine},
  title = {Pattern formation in \emph{{D}ictyostelium} via the dynamics of cooperative
	biological entities},
  journal = PRE,
  year = {1993},
  volume = {48},
  pages = {4801--4804},
  number = {6}
}

@ARTICLE{KHOR93,
  author = {H. Gobind Khorana},
  title = {Two light-transducing membrane proteins: {B}acteriorhodopsin and
	the mammalian rhodopsin},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {1166--1171}
}

@ARTICLE{BURL93,
  author = {J.~L.~Kim and D.~B.~Nikolov and S.~K.~Burley},
  title = {Co--crystal structure of {TBP} recognizing the minor groove of a
	{TATA} element},
  journal = NAT,
  year = {1993},
  volume = {365},
  pages = {520--527},
  annote = {appears to be similar system and results as the above article, this
	protein binds in the minor groove}
}

@ARTICLE{SIGL93,
  author = {Y.~Kim and J.~H.~Geiger and S.~Hahn and P.~B.~Sigler},
  title = {Crystal structure of a yeast {TBP/TATA}--box complex.},
  journal = NAT,
  year = {1993},
  volume = {365},
  pages = {512--520},
  annote = {2.5 ang crystal struct of yeast TATA box binding protein with 12bp
	show a wide open underwound, shallow minor groove, severe bend (approx
	100degrees) and postive write radically alter the B-form DNA forming
	this complex is vital in preinitiation complex on eukaryoctic RNA
	polymerase II promoters, should also include the following article}
}

@ARTICLE{KING93,
  author = {C-Y. King and M. A. Weiss},
  title = {The {SRY} high-mobility-group box recognizes {DNA} by partial intercalation
	in the minor groove: {A} topological mechanism of sequence specificity},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {11990--11994}
}

@ARTICLE{KINO93,
  author = {Henry J. Kinosian and Lynn A. Selden and James E. Estes and Lewis
	C. Gershman},
  title = {Nucleotide Binding to Actin},
  journal = JBC,
  year = {1993},
  volume = {268},
  pages = {8683--8691}
}

@ARTICLE{KNEG93,
  author = {R.~M.~A.~Knegtel and M.~Katahira and J.~G.~Schilthuis and R.~Boelens
	and and D.~Eib and P.~T.~van der Saag and R.~Kaptein},
  title = {The solution structure of the human retinoic acid receptor-$\beta$
	{DNA}-binding domain},
  journal = {J.\ Biol.\ {NRM}},
  year = {1993},
  volume = {3},
  pages = {1--17}
}

@ARTICLE{KNIG93,
  author = {D. R. Knighton and D. L. Cadena and J. Zheng and L. F. {Ten Eyck}
	and S. S. Taylor and J. M. Sowadski and G. N. Gill},
  title = {Structural features that specify tyrosine kinase activity deduced
	from homology modeling of the epidermal growth factor receptor},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {5001--5005}
}

@ARTICLE{KoHo93,
  author = {J. M. V. A. Koelman and P. J. Hoogerbrugge},
  title = {Dynamic Simulations of Hard-Sphere Suspensions Under Steady Shear},
  journal = EPL,
  year = {1993},
  volume = {21},
  pages = {363},
  annote = {referenced by EsWa95, the second paper that talks about DPD model.
	title missing.}
}

@ARTICLE{KoSu93,
  author = {R.E. Kozack and S. Subramaniam},
  title = {Brownian Dynamics Simulations of Molecular Recognition in an Antibody--Antigen
	System},
  journal = {Protein Sci.},
  year = {1993},
  volume = {2},
  pages = {915--926}
}

@ARTICLE{KRAU93,
  author = {Krauss, N. and Hinrichs, W. and Witt, I. and Fromme, P. and Pritzkow,
	W. and Dauter, Z. and Betzel, C. and Wilson, K. S. and Witt, H. T.
	and Saenger, W.},
  title = {3-Dimensional Structure of System-{I} of Photosynthesis at 6 Angstrom
	Resolution},
  journal = NAT,
  year = {1993},
  volume = {361},
  pages = {326--331},
  number = {6410},
  abstract = {X-ray structure analysis shows that the monomer of trimeric photosystem
	I (PS I) of Synechococcus sp. consists of a catalytic domain and
	a smaller domain that connects the monomers. The 4Fe-4S clusters
	F(X), F(A) and F(B), 28 alpha-helices and 45 chlorophyll a molecules
	were located. The two large subunits of PS I are represented by nine
	alpha-helices each; they are related by a local 2-fold rotation axis
	passing through F(X). Electron densities close to this axis are interpreted
	as carriers of the electron transfer chain.},
  address = {free univ berlin,inst kristallog,takustr 6, w-1000 berlin 33, germany.
	tech univ berlin,max volmer inst biophys \& phys chem, w-1000 berlin
	12, germany. desy,european molec biol lab outstn, w-2000 hamburg
	52, germany.},
  annote = {requested Tx=19930216.},
  keywords = {cyanobacterium-synechococcus-sp. pigment-protein-complexes. primary-electron-donor.
	photosystem-i. rhodopseudomonas-viridis. thylakoid-membrane. crystallization.
	identification. orientation. crystallography.}
}

@ARTICLE{KREB93,
  author = {Mark P. Krebs and H. Gobind Khorana},
  title = {Mechanism of Light-Dependent Proton Translocation by Bacteriorhodopsin},
  journal = {J. Bacteriol.},
  year = {1993},
  volume = {175},
  pages = {1555--1560}
}

@ARTICLE{KURR93,
  author = {Christian Kurrer and Klaus Schulten},
  title = {Dependence of Percolation Thresholds on Lattice Connectivity},
  journal = PRE,
  year = {1993},
  volume = {48},
  pages = {614--617},
  number = {1},
  annote = {Early title was ``Dependence of Percolation Thresholds on the Lattice
	Coordination Number''},
  tbtechrep = {TB-93-02}
}

@BOOK{LaFi93,
  title = {A Scientist's and Engineers Guide to Workstations and Supercomputers
	Coping with $\mbox{Unix}^{TM}$, RISC, vectors, and programming},
  publisher = {John Wiley and Sons},
  year = {1993},
  author = {R.H. Landau and {P.J. Fink, Jr.}},
  nremark = {"good book for CSE", ISBN="0-471-53271-1 (paper)", call_nu="004.0245
	L231S"}
}

@ARTICLE{LAND93,
  author = {D. Landsman and M. Bustin},
  title = {A signature for the {HMG-1} box {DNA}-binding proteins},
  journal = {BioEssays},
  year = {1993},
  volume = {15},
  pages = {539--546},
  number = {8}
}

@ARTICLE{LANY93,
  author = {J. K. Lanyi},
  title = {Proton Translocation Mechanism and Energetics in the Light-Driven
	Pump Bacteriorhodopsin},
  journal = BBA,
  year = {1993},
  note = {submitted}
}

@ARTICLE{LASK93,
  author = {R. A. Laskowski and M. W. MacArthur and D. S. Moss and J. M. Thornton},
  title = {{PROCHECK}: a program to check the stereochemical quality of protein
	structures},
  journal = JAC,
  year = {1993},
  volume = {26},
  pages = {283--291}
}

@ARTICLE{LAWS93,
  author = {C.~L.~Lawson and J.~Carey.},
  title = {Tandem binding in crystals of a {it trp} repressor/operator half-site
	complex},
  journal = NAT,
  year = {1993},
  volume = {366},
  pages = {178--182}
}

@ARTICLE{LAZA93,
  author = {M.~A.~Lazar},
  title = {Thyroid hormone receptors: multiple forms, multiple possibilities.},
  journal = ER,
  year = {1993},
  volume = {14},
  pages = {184--193}
}

@ARTICLE{LEE93,
  author = {M.~S.~Lee and S.~A.~Kliewer and J.~Provencal and P.~Wright and R.~M.~Evans},
  title = {Structure of the retinoid X receptor $\alpha$ {DNA} binding domain:
	a helix required for homodimeric {DNA} binding},
  journal = SCI,
  year = {1993},
  volume = {260},
  pages = {1117--1121}
}

@ARTICLE{LEIG93,
  author = {Leigh, W J},
  title = {{Merck-Frosst} Award Lecture: {Orbital} Symmetry and the Photochemistry
	of Cyclobutene},
  journal = {Can. J. Chem.},
  year = {1993},
  volume = {71},
  pages = {147--155}
}

@ARTICLE{LEVI93,
  author = {M.~Levitt and B.~H.~Park},
  title = {Water: now you see it, now you don't},
  journal = {Structure},
  year = {1993},
  volume = {1},
  pages = {223--226},
  annote = {review of techniques and measures of water}
}

@BOOK{LiBo93,
  title = {Reviews in Computational Chemistry},
  publisher = {VCH Publishers},
  year = {1993},
  author = {K. B. Lipkowitz and D.B. Boyd},
  volume = {1-4},
  address = {Weinheim},
  nremark = {molecular mechanics, introduction, force field}
}

@ARTICLE{LiBe93,
  author = {Z. Liu and B. J. Berne},
  title = {Method for Accelerating Chain Folding and Mixing},
  journal = JCP,
  year = {1993},
  volume = {99},
  pages = {6071--6077},
  number = {8},
  abstract = {An algorithm based on allowing the form of the intermolecular potential
	to fluctuate is introduced into molecular dynamics and {M}onte {C}arlo
	simulations. It is shown that this method accelerates the approach
	to equilibrium in frustrated systems. It provides a very useful method
	for determining all of the local minima in complex systems. Examples
	are mixing in dense binary liquids and folding of long polymer chains.
	When this method is combined with umbrella sampling techniques it
	accelerates the simulations of a wide class of chemically important
	systems.},
  annote = {fluctuating potential method, in Schu99}
}

@ARTICLE{LIVN93,
  author = {N. Livnah and M. Sheves},
  title = {Model Compounds Can Mimic Spectroscopic Properties of Bovine Rhodopsin},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {351--353}
}

@ARTICLE{LIVN93A,
  author = {Oded Livnah and Edward A. Bayer and Meier Wilchek and Joel L. Sussman},
  title = {Three-dimensional structures of avidin and the avidin-biotin complex},
  journal = BCH,
  year = {1993},
  volume = {90},
  pages = {5076--5080},
  annote = {june 1}
}

@INPROCEEDINGS{LTGB93,
  author = {P.~S. Lomdahl and P. Tamayo and N. Gr{\o}nbec{h-J}ensen and D.~M.
	Beazley},
  title = {50 {G-F}lops Molecular Dynamics on the {C}onnection {M}achine},
  booktitle = {Proceedings of Supercomputing~'93},
  year = {1993},
  pages = {520--527},
  organization = {IEEE Computer Society}
}

@ARTICLE{LORE93,
  author = {M. Lorenz and D. Popp and K. C. Holmes},
  title = {Refinement of the {F}-Actin Model against {X}-ray Fiber Diffraction
	Data by the Use of a Directed Mutation Algorithm},
  journal = JMB,
  year = {1993},
  volume = {234},
  pages = {826--836}
}

@ARTICLE{XPLU93,
  author = {X.~P.~Lu and N.~L.~Eberhardt and M.~Pfahl},
  title = {{DNA} Bending by Retinoid X Receptor--Containing Retinoid and Thyroid
	Hormone Receptor Complexes},
  journal = MCB,
  year = {1993},
  volume = {13},
  pages = {6509--6519},
  number = {10},
  annote = {bending of {DNA}induced by various combos of TR,RXR,RAR }
}

@ARTICLE{LUND93,
  author = {T.~Lundb{\"a}ck and C.~Cairns and J.~A.~Gustafsson and J.~Carlstedt-Duke
	and T.~H{\"a}rd},
  title = {Thermodynamics of the glucocorticoid receptor--{DNA} interaction:
	binding of wild-type {GR DBD} to different response elements.},
  journal = BCHJ,
  year = {1993},
  volume = {32},
  pages = {5074--5082}
}

@ARTICLE{LYLE93,
  author = {P. A. Lyle and S. V. Kolaczkowski and G. J. Small},
  title = {Photochemical Hole-Burned Spectra of Protonated and Deuterated Reaction
	Centers of {\em Rhodobacter sphaeroides}},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {6924--6933}
}

@ARTICLE{MAHA93,
  author = {L. Mahadevan and J. B. Keller},
  title = {The shape of a {M\"obius} band},
  journal = PRSLA,
  year = {1993},
  volume = {440},
  pages = {149--162}
}

@ARTICLE{MAIE93,
  author = {E.J. Maier and J.K. Bowmaker},
  title = {Colour vision in the passerine bird {\em {L}eiothrix lutea}: correlation
	of visual pigments absorbance and oil droplet transmission with spectral
	sensitivity},
  journal = {J.~Comp.~Physiol.},
  year = {1993},
  volume = {172},
  pages = {295--301},
  annote = {spectral sensitivity of birds}
}

@ARTICLE{MALP93,
  author = {J. Malpeli and D. Lee and F. H. Baker},
  title = {Laminar and Retinotopic Organization of the Macaca Lateral Geniculate
	Nucleus: Magnocellular and Parvocellular Magnification Functions},
  year = {1993},
  note = {Submitted}
}

@ARTICLE{MARC93,
  author = {M. Marchi and J. N. Gehlen and D. Chandler and M. Newton},
  title = {Diabatic Surfaces and the Pathway for Primary Electron Transfer in
	a Photosynthetic Reaction Center},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {4178--4190},
  number = {10}
}

@ARTICLE{MARR93,
  author = {S.J. Marrink and M. Berkowitz and H. J. C. Berendsen},
  title = {Molecular Dynamics Simulation of a Membrane/Water Interface: The
	Ordering of Water and Its Relation to the Hydration Force},
  journal = {Langmuir},
  year = {1993},
  volume = {9},
  pages = {3122},
  number = {11}
}

@ARTICLE{MART93A,
  author = {Thomas Martinetz and Klaus Schulten},
  title = {A Neural Network for Robot Control: Cooperation Between Neural Units
	as a Requirement for Learning},
  journal = CEE,
  year = {1993},
  volume = {19},
  pages = {315--332},
  number = {4},
  annote = {Special Issue on ``Neural Networks: Theory and Applications in Robotics
	and Manufacturing''}
}

@INPROCEEDINGS{MART93C,
  author = {Thomas Martinetz and Klaus Schulten},
  title = {A Neural Network with {H}ebbian-Like Adaptation Rules Learning Visuomotor
	Coordination of a {PUMA} Robot},
  booktitle = {Proceedings of the {IEEE} International Conference on Neural Networks
	({ICNN--93}), {S}an {F}rancisco},
  year = {1993},
  pages = {820--825},
  annote = {Published in April 93. The early draft of this paper was called ``Neural
	Network with {H}ebbian-Like Adaptation Rules Learning Control of
	a {PUMA} Robot'', and included J\"org A. Walter as an author, and
	was submitted to NIPS, but was not published.}
}

@ARTICLE{MART93B,
  author = {Thomas M. Martinetz and Stanislav G. Berkovich and Klaus Schulten},
  title = {``{N}eural Gas'' for Vector Quantization and its Application to Time-Series
	Prediction},
  journal = IEEENN,
  year = {1993},
  volume = {4},
  pages = {558--569},
  number = {4},
  annote = {Formerly called MART91A, Published in the July 1993 issue.},
  tbtechrep = {TB-91-22}
}

@ARTICLE{MAVR93,
  author = {J. Mavri and H. J. C. Berendsen and W. F. Van Gunsteren},
  title = {Influence of Solvent on Intramolecular Proton Transfer in Hydrogen
	Malonate -- Molecular Dynamics Simulation Study of Tunneling by Density
	Matrix Evolution and Nonequilibrium Solvation},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {13469--13476}
}

@ARTICLE{McLa93,
  author = {Robert~I. McLachlan},
  title = {Explicit {L}ie--{P}oisson Integration and the {E}uler Equations,},
  journal = {Phys.\ Rev.\ Lett.},
  year = {1993},
  volume = {71},
  pages = {3043--3046},
  abstract = {We give a wide class of Lie-Poisson systems for which explicit, Lie-Poisson
	integrators, preserving all Casimirs, can be constructed. The methods
	are extremely simple. Examples are the rigid body, a moment truncation,
	and a new, fast algorithm for the sine-bracket truncation of the
	2D Euler equations.},
  keywords = {Lie-Poisson systems, {H}amiltonian systems, symplectic integrators,
	composition methods, operator splitting.},
  nremark = {Postscript version is available by anonymous ftp from newton.colorado.edu
	(128.138.249.1), directory pub/numerics/papers, files sine.ps.Z and
	composition.ps.Z.}
}

@ARTICLE{MeCH93,
  author = {S.~Melchionna and G.~Ciccotti and B.~L. Holian},
  title = {Hoover {NPT} Dynamics for Systems Varying in Shape and Size},
  journal = {Mol.\ Phys.},
  year = {1993},
  volume = {78},
  pages = {533--544},
  number = {3}
}

@INPROCEEDINGS{Meye93,
  author = {Y. Meyer},
  title = {Algorithms and Applications},
  booktitle = SJSSC,
  year = {1993},
  address = {Philadelphia}
}

@ARTICLE{MIAS93,
  author = {K.~Miaskiewicz and R.~Osman and H.~Weinstein},
  title = {Molecular Dynamics Simulation of the Hydrated d({CGCGAATTCGCG})$_2$
	Dodecamer},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {1526--1537},
  annote = {150ps MD, 22NA ions, water, amber, unstable ions and question the
	stability of stable {DNA}structure, 20.45 waters solvate A-T and
	21.38 solvate G-C}
}

@ARTICLE{MIYA93,
  author = {Shuichi Miyamoto and Peter A. Kollman},
  title = {Absolute and Relative Binding Free Energy Calculations of the Interaction
	of Biotin and Its Analogs With Streptavidin Using Molecular Dynamics/Free
	Energy Perturbation Approaches},
  journal = PSFG,
  year = {1993},
  volume = {16},
  pages = {226--245},
  annote = {june 1}
}

@ARTICLE{MPRO93,
  author = {Mochena, M. and M. Pollak and J. Ruiz and M. Ortu{\~n}o},
  title = {Energy and dielectric relaxation in the Coulomb gap},
  journal = {PHYSICA A (Statistical and Theoretical Physics)},
  year = {1993},
  volume = {201},
  pages = {178},
  number = {Nos.~1, 2 and 3},
  nremark = {Proceedings of the International Workshop on Dynamics of Disordered
	Materials II, held in Grenoble, France on March 22 - 24, 1993 CHAPTER
	4. COMPUTER SIMULATION}
}

@ARTICLE{MOUR93,
  author = {O.G. Mouristen},
  title = {Models of lipid-protein interactions in membranes},
  journal = {Annu. Rev. Biophys. Biomol. Struct.},
  year = {1993},
  volume = {22},
  pages = {145--171}
}

@ARTICLE{MUNR93,
  author = {U. Munro and W. Wiltschko},
  title = {Magnetic compass orientation in the yellow-faced honeyeater, {\em
	Lichenostomus chrysops}, a day-migrating bird from Australia},
  journal = {Behav.~Ecol.~Sociobiol.},
  year = {1993},
  volume = {32},
  pages = {141--145}
}

@INPROCEEDINGS{MURR93,
  author = {J. D. Murray},
  title = {Mathematical Biology, Second Corrected Edition},
  booktitle = {Biomathematics},
  year = {1993},
  volume = {19},
  pages = {156,376,406,472,739},
  address = {Berlin, Heidelberg},
  publisher = {Springer-Verlag}
}

@ARTICLE{NAGA93,
  author = {H. Nagae and T. Kakitani and T. Katohi and M. Mimuro},
  title = {Calculation of the excitation transfer matrix elements between the
	{S}$_2$ or {S}$_1$ state of carotenoid and the {S}$_2$ or {S}$_1$
	state of bacteriochlorophyll},
  journal = JCP,
  year = {1993},
  volume = {98},
  pages = {8012--8023}
}

@ARTICLE{NARD93,
  author = {A.~M.~Nardulli and G.~L.~Greene and D.~J.~Shapiro},
  title = {Human Estrogen Receptor Bound to an Estrogen Response Element Bends
	{DNA}.},
  journal = {Molecular Endocrinology},
  year = {1993}
}

@ARTICLE{NARD,
  author = {A.~M.~Nardulli and D.~J.~Shapiro},
  title = {{DNA} Bending by Nuclear Receptors},
  journal = {Receptor},
  year = {1993},
  volume = {3},
  pages = {247--255},
  annote = {more bending of 36\degree by nardulli and shapiro}
}

@TECHREPORT{Neal93,
  author = {R. M. Neal},
  title = {Probabilistic inference using {M}arkov chain {M}onte {C}arlo methods},
  institution = {University of Toronto},
  year = {1993},
  number = {CRG-TR-93-1},
  annote = {papers available from \texttt{http://www.cs.toronto.edu/\~{}radford/papers-online.html}}
}

@TECHREPORT{NSF07,
  author = {Cyberinfrastructure Council},
  title = {Cyberinfrastructure Vision for 21st Century Discovery},
  institution = {National Science Foundation},
  year = {2007},
  month = {March},
  number = {1}
}

@ARTICLE{NINA93,
  author = {M. Nina and J.C. Smith and B. Roux},
  title = {Ab initio quantum chemical analysis of {Schiff} base-water interactions
	in bacteriorhodopsin},
  journal = JMS,
  year = {1993},
  volume = {105},
  pages = {231--245}
}

@ARTICLE{NOEL93,
  author = {J. P. Noel and H. E. Hamm and P. B. Sigler},
  title = {The 2.2\,{{\AA}} crystal structure of transducin complexed with {GTP$\gamma$S}},
  journal = NAT,
  year = {1993},
  volume = {366},
  pages = {654--663}
}

@ARTICLE{NONE93,
  author = {M. Nonella and D. Oesterhelt},
  title = {Structure of Bacteriorhodopsin and the Effect of Mutation of Asp-85
	or Asp-212 on Structure, Spectrum and Electrostatics: A Computational
	Study},
  year = {1993},
  note = {submitted}
}

@ARTICLE{NTMB93,
  author = {S. S. Northrup and K. A. Thomasson and C. M. Miller and P. D. Barker
	and L. D. Eltis and J. G. Guillemette and S. C. Inglis and A. G.
	Mark},
  title = {Effects of charged amino acid mutations on the bimolecular kinetics
	of reduction of yeast iso-1-ferricytochrome c by bovine ferrocytochrome
	b5},
  journal = {Biochem.},
  year = {1993},
  volume = {32},
  pages = {6613--6623},
  number = {26}
}

@ARTICLE{OBY-93,
  author = {Klaus Obermayer and Gary G. Blasdel},
  title = {Geometry of Orientation and Ocular Dominance Columns in Monkey Striate
	Cortex},
  journal = JN,
  year = {1993},
  volume = {13},
  pages = {4114--4129},
  annote = {The early version of the paper was titled `Development of Orientation
	and Ocular Dominance Columns and Dimension Reducing Mappings: A Comparison
	between Theory and Experiment'. That version was rejected by a journal,
	and the paper was revised and resubmitted to J. Neuroscience under
	a new title and without KS as an author.}
}

@ARTICLE{Okun93,
  author = {D. Okunbor},
  title = {Variable step size does not harm second-order integrators for {H}amiltonian
	systems},
  journal = {J. Comput.\ Appl.\ Math.},
  year = {1993},
  volume = {47},
  pages = {273--279},
  number = {2},
  nremark = {"% doubt about whether 273 is a page number", "Letter"}
}

@ARTICLE{OLIV93,
  author = {M. Ollivuci and I. Ragazos and F. Bernardi and M. Robb},
  title = {A Conical Intersection Mechanism for the Photochemistry of Butadiene.
	A {MC-SCF} Study.},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {3710--3721}
}

@ARTICLE{OLSO93,
  author = {Wilma K. Olson and Nancy L. Marky and Robert L. Jernigan and Victor
	B. Zhurkin},
  title = {Influence of fluctuations on {DNA} curvature. {A} comparison of flexible
	and static wedge models of intrinsically bent {DNA}},
  journal = JMB,
  year = {1993},
  volume = {232},
  pages = {530--554}
}

@ARTICLE{Orengo93,
  author = {C. A. Orengo and T. P. Flores and W. R. Taylor and J. M. Thornton},
  title = {Identification and Classification of Protein Fold Families},
  journal = {Prot. Eng.},
  year = {1993},
  volume = {6},
  pages = {485--500}
}

@ARTICLE{ORLO93,
  author = {A. Orlova and E. H. Egelman},
  title = {A conformational change in the actin subunit can change the flexibility
	of the actin filament},
  journal = JMB,
  year = {1993},
  volume = {232},
  pages = {334--341}
}

@BOOK{Ott93,
  title = {Chaos in Dynamical Systems},
  publisher = {C U P},
  year = {1993},
  author = {Edward Ott}
}

@ARTICLE{OtLW93,
  author = {Gottfried Otting and Edvards Liepinsh and Kurt Wuthrich},
  title = {Disulfide Bond Isomerization in BPTI and BPTI(G36S): An NMR Study
	of Correlated Mobility in Proteins},
  journal = {Biochemistry},
  year = {1993},
  volume = {32},
  pages = {3571--3582}
}

@ARTICLE{PaHo93,
  author = {Alexandre Panfilov and Pauline Hogeweg},
  title = {Spiral breakup in a modified FitzHugh-Nagumo model},
  journal = {Phys. Lett. A},
  year = {1993},
  volume = {176},
  pages = {295--299}
}

@INPROCEEDINGS{PAST93,
  author = {R. W. Pastor and R. M. Venable},
  title = {Molecular and Stochastic dynamics simulation of lipid molecules},
  booktitle = {Computer simulation of biomolecular systems: Theoretical and experimental
	applications},
  year = {1993},
  editor = {W. F. van Gunsteren and P. K. Weiner and A. K. Wilkinson},
  note = {In press}
}

@ARTICLE{PAUL93,
  author = {T. T. Paull and M. J. Haykinson and R. C. Johnson},
  title = {The nonspecific {DNA-}binding and -bending proteins {HMG1} and {HMG2}
	promote the assembly of complex nucleoprotein structures},
  journal = {Genes and Development},
  year = {1993},
  volume = {7},
  pages = {1521--1534}
}

@ARTICLE{PEAR93,
  author = {D.~Pearce and K.~R.~Yamamoto},
  title = {Mineralcorticoid and Glucocorticoid Receptor Activities Distinguish
	by Nonreceptor Factors at a Composite Response Element},
  journal = SCI,
  year = {1993},
  volume = {259},
  pages = {1161--1165},
  annote = {it's a report, suggests additional factors affect as title suggest}
}

@ARTICLE{PHIL93,
  author = {J.B. Phillips and O. Sayeed},
  title = {Wavelength-dependent effects of light on magnetic compass orientation
	in {\em {D}rosophila melanogaster}},
  journal = {J.~.Comp.~Physiol.~A},
  year = {1993},
  volume = {172},
  pages = {303--308}
}

@ARTICLE{PiKr93,
  author = {Pistoor, N. and K. Kremer},
  title = {Structure and dynamics of Yukawa systems},
  journal = {PHYSICA A (Statistical and Theoretical Physics)},
  year = {1993},
  volume = {201},
  pages = {171},
  number = {Nos.~1, 2 and 3},
  nremark = {Proceedings of the International Workshop on Dynamics of Disordered
	Materials II, held in Grenoble, France on March 22 - 24, 1993 CHAPTER
	4. COMPUTER SIMULATION}
}

@ARTICLE{PoCr93,
  author = {J.~W. Powell and R.~E. Crandall},
  title = {Lattice dynamics for a simplified DNA model},
  journal = {Mathematica in Education},
  year = {1993},
  volume = {2},
  pages = {15--20i},
  number = {3}
}

@ARTICLE{PREV93,
  author = {C.~Prevost and S.~Louise-May and G.~Ravishanker and R.~Lavery and
	D.~L.~Beveridge},
  title = {Persistence Analysis of the Static and Dynamical Helix Deformations
	of {DNA} Oligonucleotides: Applications to the Crystal Structure
	and Molecular Dynamics Simulation of d({CGCGAATTCGCG})$_2$},
  journal = BP,
  year = {1993},
  volume = {33},
  pages = {335--350},
  annote = {persistence length and flexibility analysis of DNA, measures of bending
	and orientation of bps,}
}

@ARTICLE{PUGL93,
  author = {Luisa Pugliese and Alessandro Coda and Massimo Malcovati and Martino
	Bolognesi},
  title = {Three-dimensional Structure of the Tetragonal Crystal Form of Egg-white
	Avidin in its Functional Complex with Biotin at {2.7 {\AA}} Resolution},
  journal = JMB,
  year = {1993},
  volume = {231},
  pages = {698--710},
  annote = {june 1}
}

@ARTICLE{PUHL93,
  author = {H.~L.~Puhl and M.~J.~Behe},
  title = {Structure of nucleosomal {DNA} at high salt concentrations as probed
	by hydroxyl radical},
  journal = JMB,
  year = {1993},
  volume = {229},
  pages = {827--832},
  annote = {same conclusion as HAYE90}
}

@ARTICLE{QIU93,
  author = {X. Qiu and C. Pidgeon},
  title = {A $^{ 31}$P {NMR} study of immobilized artificial membrane surfaces:
	structure and dynamics of immobilized phospholipids},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {12399--12407}
}

@ARTICLE{RAMA93,
  author = {V.~Ramakrishnan and J.~T.~Finch and V.~Graziano and P.~L.~Lee and
	R.~M.~Sweet},
  title = {Crystal structure of globular domain of histone H5 and its implications
	for nucleosome binding},
  journal = NAT,
  year = {1993},
  volume = {362},
  pages = {219--223},
  annote = {cross ref with WOLF94, 2.5{\AA\ }, similar to DBD of catabolit gene
	acitvator protein CAP}
}

@ARTICLE{RATH93,
  author = {P. Rath and M. P. Krebs and Y. He and H. G. Khorana and K. J. Rothschield},
  title = {Fourier Transform Raman Spectroscopy of the Bacteriorhodopsin Mutant
	Tyr-185 {$\rightarrow$} Phe: Formation of a Stable O-like Species
	during Light Adaptation and Detection of Its Transient N-like Photoproduct},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {2272--2281}
}

@ARTICLE{RATH93a,
  author = {P. Rath and T. Marti and S. Sonar and H. G. Khorana and K. J. Rothschild},
  title = {Hydrogen Bonding Interactions with the Schiff Base of Bacteriorhodopsin},
  journal = JBC,
  year = {1993},
  volume = {268},
  pages = {17742--17749}
}

@ARTICLE{RAYM93,
  author = {I. Rayment and W. R. Rypniewski and K. Schmidt-B{\"a}se and R. Smith
	and D. R. Tomchick and M. M. Benning and D. A. Winkelmann and G.
	Wesenberg and H. M. Holden},
  title = {Three-Dimensional Structure of Myosin Subfragment-1: A Molecular
	Motor},
  journal = SCI,
  year = {1993},
  volume = {261},
  pages = {50--58}
}

@ARTICLE{READ93,
  author = {C. M. Read and P. D. Cary and C. {Crane-Robinson} and P. C. Driscoll
	and D. G. Norman},
  title = {Solution structure of a {DNA}-binding domain from {HMG1}},
  journal = NAR,
  year = {1993},
  volume = {21},
  pages = {3427--3436},
  number = {15}
}

@TECHREPORT{Reic93a,
  author = {S. Reich},
  title = {Symplectic integration of constrained {H}amiltonian systems by Runge-Kutta
	methods},
  institution = {Dept. Computer Sci., Univ.\ of British Columbia},
  year = {1993},
  number = {93-13},
  nremark = {% cite LeSk}
}

@ARTICLE{RJLT93,
  author = {R.~D. Riddle and R.~L. Johnson and E.~Laufer and C.~Tabin},
  title = {Sonic hedgehog mediates the polarizing activity of the ZPA},
  journal = {Cell},
  year = {1993},
  volume = {75},
  pages = {1401--1416},
  number = {7}
}

@MISC{MURC93,
  author = {Murco N. Ringnalda and Jean-Marc Langlois and Burnham H. Greeley
	and Thomas V. Russo and Richard P. Muller and Bryan Marten and Youngdo
	Won and Robert E. Donnelly, Jr. and W. Thomas Pollard and Gregory
	H. Miller and William A. Goddard III and and Richard A. Friesner},
  title = {PS-GVB v0.08},
  howpublished = {Schroedinger Inc.},
  year = {1993},
  annote = {PSGVB program used by Todd Martinez}
}

@ARTICLE{RODG93,
  author = {D.~W.~Rodgers and S.~C.~Harrison},
  title = {The complex between phage 434 repressor {DNA}--binding domain and
	operator site {O}$_{R}$3: structural differences between consensus
	and non-consensus half-sites.},
  journal = STR,
  year = {1993},
  volume = {1},
  pages = {227--240}
}

@ARTICLE{ROMB93,
  author = {L. Romberg and R.D. Vale},
  title = {Chemomechanical cycle of kinesin differs from that of myosin},
  journal = NAT,
  year = {1993},
  volume = {361},
  pages = {168--170}
}

@ARTICLE{ROOS94,
  author = {B. Roos and M. Merchan and R. McDiarmid and X. Xing},
  title = {Theoretical and Experimental Determination of the Electrinic Spectrum
	of Norboradiene.},
  journal = JACS,
  year = {1993},
  volume = {116},
  pages = {5927--5936}
}

@ARTICLE{ROOS93,
  author = {B. Roos and L. Serranoandres and M. Merchan},
  title = {Multiconfigurational 2nd Order Pertubation Theory Applied to the
	Calculation of Electronic Spectra of Conjugated Systems.},
  journal = PAC,
  year = {1993},
  volume = {65},
  pages = {1693--1698}
}

@ARTICLE{SALI93,
  author = {A. Sali and T. L. Blundell},
  title = {Comparative protein modelling by satisfaction of spatial restraints},
  journal = JMB,
  year = {1993},
  volume = {234},
  pages = {779}
}

@INCOLLECTION{SANK93,
  author = {M.B. Sankaram and D. Marsh},
  title = {Protein--lipid interactions with peripheral membrane proteins},
  booktitle = {Protein--lipid interactions},
  publisher = {Elsevier Science Publishers},
  year = {1993},
  editor = {A. Watts},
  pages = {127--162},
  address = {New York}
}

@ARTICLE{SASA93,
  author = {J. Sasaki and A. Maeda},
  title = {Time-Resolved Infrared Spectral Analysis of the {KL}-to-{L} Conversion
	in the Photocycle of Bacteriorhodopsin},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {867--871}
}

@ARTICLE{Schi93,
  author = {J.~P. Schiffer},
  title = {Phase Transitions in Anisotropically Confined Ionic Crystals},
  journal = PRL,
  year = {1993},
  volume = {70},
  pages = {818--821},
  number = {6}
}

@ARTICLE{SCHL93,
  author = {J. Schlitter and M. Engels and P. Kr{\"u}ger and E. Jacoby and A.
	Wollmer},
  title = {Targeted Molecular Dynamics Simulation of Conformational Change -
	Application to the {T $\leftrightarrow$ R} Transition in Insulin},
  journal = MS,
  year = {1993},
  volume = {10},
  pages = {291--308},
  number = {2--6}
}

@ARTICLE{SCHN93,
  author = {B.~Schneider and D.~M.~Cohen and L.~Schleifer and A.~R.~ Srinivasan
	and W.~Olson and H.~M.~Berman},
  title = {A Systematic Method for Studying the Spatial Distribution of Water
	Molecules around Nucleic Acid Bases},
  journal = BJ,
  year = {1993},
  volume = {65},
  pages = {2291--2303},
  annote = {hydrated building blocks for constructing solvated DNA's based on
	studies from known crystal structures.}
}

@ARTICLE{SCHU93,
  author = {C. E. Schutt and J. C. Myslik and M. D. Rozycki and N. C. W. Goonesekere
	and U. Lindberg},
  title = {The structure of crystalline profilin-${\beta}$-actin},
  journal = NAT,
  year = {1993},
  volume = {365},
  pages = {810--816}
}

@ARTICLE{SCHW93,
  author = {J.~W.~R.~Schwabe and L.~Chapman and J.~T.~Finch and D.~Rhodes},
  title = {The Crystal Structure of the Estrogen Receptor {DNA}-Binding Domain
	Bound to {DNA}: How Receptors Discriminate between Their Response
	Elements},
  journal = {Cell},
  year = {1993},
  volume = {75},
  pages = {567--578},
  number = {5},
  annote = {this is the crsytal struct of estrogen receptor {2.4\,\AA} resolution}
}

@ARTICLE{SCHW93A,
  author = {J.~W.~R.~Schwabe and L.~C.~Chapman and J.~T.~Finch and D.~Rhodes
	and D.~Neuhaus},
  title = {{DNA} recognition by the estrogen receptor: from solution to the
	crystal},
  journal = {Structure},
  year = {1993},
  volume = {15},
  pages = {187--204},
  annote = {some interesting discussion on the role of cooperativity and the
	relationship to structure of the dimer region ie dimerization give
	structure to unstructured solution}
}

@ARTICLE{SCHW93B,
  author = {J.~W.~R.~Schwabe and L.~Fairall and L.~Chapman and J.~T.~Finch and
	R.~N.~Dutnall and D.~Rhodes},
  title = {Two cocrystal structures of two zinc--stabilized {DNA}--binding domains
	illustrate different ways of achieving sequence--specific {DNA} recognition.},
  year = {1993},
  volume = {LVIII},
  pages = {141--147},
  address = {UK},
  booktitle = {Cold Spring Harbor Symposia on Quantitative Biology},
  publisher = {Cold Spring Harbor Laboratory Press}
}

@ARTICLE{ScHe93,
  author = {J. L. Scully and J. Hermans},
  title = {Multiple time steps: Limits on the speedup of molecular dynamics
	simulations in aqueous systems},
  journal = {Mol.\ Simulation},
  year = {1993},
  volume = {11},
  pages = {67--77}
}

@ARTICLE{SERR93B,
  author = {L. Serrano-Andreas and R. Lindh and B. Roos and M. Merchan},
  title = {Theoretical Study of the Electronic Spectrum of All-Tran-1,3,5,7-Octatetraene.},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {9360--9368}
}

@ARTICLE{SERR93A,
  author = {L. Serrano-Andreas and M. Merchan and I. Nebot-Gil and I. Nebot-Gil
	and B. Roos},
  title = {Towards an Accurate Molecular Orbital Theory for Ecited States: Ethene,
	Butadiene, and Hexatriene.},
  journal = JCP,
  year = {1993},
  volume = {98},
  pages = {3151--3162}
}

@ARTICLE{SERR93,
  author = {L. Serrano-Andreas and M. Merchan and I. Nebot-Gil and B. Roos and
	M. Fulscher},
  title = {Theoretical Study of Electronic Spectra of Cyclopentadiene, Pyrrole,
	and Furan.},
  journal = JACS,
  year = {1993},
  volume = {115},
  pages = {6184--6197}
}

@ARTICLE{KOST93,
  author = {R. Sessions and P. Dauber-Osguthorpe and D. Osguthorpe},
  title = {Effect of Various Frictional Models on Long-Time Peptide Dynamics},
  journal = BP,
  year = {1993},
  volume = {33},
  pages = {1423--1429}
}

@ARTICLE{SIPP93,
  author = {M. J. Sippl},
  title = {Boltzmann's Principle, Knowledge Based Mean Fields and Protein Folding.
	{A}n Approach to the Computational Determination of Protein Structures},
  journal = {J. Computer Aided Mol. Design},
  year = {1993},
  volume = {7},
  pages = {473--501}
}

@ARTICLE{Skee93,
  author = {R.~D. Skeel},
  title = {Variable Step Size Destabilizes the {S}t{\"o}rmer/Leapfrog/{Verlet}
	Method},
  journal = {BIT},
  year = {1993},
  volume = {33},
  pages = {172--175}
}

@INPROCEEDINGS{SkBO93,
  author = {R.~D. Skeel and J. Biesiadecki and D. Okunbor},
  title = {Symplectic integration for macromolecular dynamics},
  booktitle = {Proceedings of the International Conference on Computation of Differential
	Equations and Dynamical Systems},
  year = {1993},
  editor = {Kang Feng and Zhong-Ci Shi},
  pages = {49--61},
  address = {Singapore},
  publisher = {World Scientific Publishing Co.},
  nack = {NSF90},
  nremark = {Beijing P. R. China, September 1--5}
}

@BOOK{SkKe93,
  title = {Elementary Numerical Computing with Mathematica},
  publisher = {McGraw-Hill},
  year = {1993},
  author = {R.~D. Skeel and Jerry B. Keiper},
  address = {New York}
}

@INPROCEEDINGS{SMAG93,
  author = {Patrick van der Smagt and Klaus Schulten},
  title = {Control of Pneumatic Robot Arm Dynamics by a Neural Network},
  booktitle = {Proceedings of the World Congress on Neural Networks, Portland, OR,
	July 11-15},
  year = {1993},
  volume = {3},
  pages = {180--183}
}

@BOOK{Smit93,
  title = {The Design and Analysis of Parallel Algorithms},
  publisher = {Oxford Univ.\ Press},
  year = {1993},
  author = {Justin R. Smith},
  address = {New York}
}

@ARTICLE{Smit99,
  author = {Paul E. Smith},
  title = {The alanine dipeptide free energy surface in solution},
  journal = JCP,
  year = {1993},
  volume = {111},
  pages = {5568--5579}
}

@ARTICLE{SMIT92,
  author = {P. E. Smith and R. M. Brunne and A. E. Mark and W. F. van Gunsteren},
  title = {Dielectric Properties of Trypsin Inhibitor and Lysozyme Calculated
	from Molecular Dynamics Simulations},
  journal = JPC,
  year = {1993},
  volume = {97},
  pages = {2009--2014}
}

@ARTICLE{SmHa93,
  author = {Smolej, F. and H.H. Hahn},
  title = {Numerical investigations of mode coupling approximations for the
	glass transition in Lennard-Jones systems},
  journal = {PHYSICA A (Statistical and Theoretical Physics)},
  year = {1993},
  volume = {201},
  pages = {164},
  number = {Nos.~1, 2 and 3},
  nremark = {Proceedings of the International Workshop on Dynamics of Disordered
	Materials II, held in Grenoble, France on March 22 - 24, 1993 CHAPTER
	4. COMPUTER SIMULATION}
}

@ARTICLE{SONG93,
  author = {L. Song and M. A. El-Sayed and J. K. Lanyi},
  title = {Protein Catalysis of the Retinal Subpicosecond Photo-isomerization
	in the Primary Process of Bacteriorhodopsin Photosynthesis},
  journal = SCI,
  year = {1993},
  volume = {261},
  pages = {891--894}
}

@ARTICLE{SORC93,
  author = {M. Sorci-Thomas and M. W. Kearns and J. P. Lee},
  title = {Apolipoprotein {A-I} Domains Involved in Lecithin-Cholesterol Acyltransferase
	Activation},
  journal = JBC,
  year = {1993},
  volume = {268},
  pages = {21403--21409}
}

@ARTICLE{SOTE93A,
  author = {A. Soteriou and A. Clarke and S. MArtin and J. Trinick},
  title = {Titin folding energy and elasticity},
  journal = PRSLB,
  year = {1993},
  volume = {254},
  pages = {83--86}
}

@ARTICLE{SOTE93,
  author = {A. Soteriou and M. Gamage and J. Trinick},
  title = {A survey of interactions made by the giant protein titin},
  journal = JOCS,
  year = {1993},
  volume = {104},
  pages = {119--123}
}

@ARTICLE{SPER93,
  author = {M.M. Sperotto and O.G. Mouritsen},
  title = {Lipid enrichment and selectivity of integral membrane proteins in
	two-component lipid bilayers},
  journal = {Eur Biophys J},
  year = {1993},
  volume = {22},
  pages = {323--328}
}

@ARTICLE{STEI93,
  author = {P. J. Steinbach and B. R. Brooks},
  title = {Protein hydration elucidated by molecular dynamics simulation},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {9135--9139}
}

@ARTICLE{STEW93,
  author = {R.J. Stewart and J.P. Thaler and L.S.B. Goldstein},
  title = {Direction of microtubule movement is an intrinsic property of the
	motor domain of kinesin heavy chain and {{\em Drosophila}} ncd protein},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {5209--5213}
}

@ARTICLE{PAST93A,
  author = {T. R. Stouch},
  title = {Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular
	Dynamics Simulations of Hydrated Phospholipid Bilayers},
  journal = MS,
  year = {1993},
  volume = {10},
  pages = {335--362}
}

@ARTICLE{STOU93,
  author = {T. R. Stouch},
  title = {Lipid membrane structure and dynamics studied by all-atom molecular
	dynamics simulations of hydrated phospholipid bilayers},
  journal = {Molecular Simulation},
  year = {1993},
  note = {In press}
}

@ARTICLE{SUBR93,
  author = {S. Subramanian and M. Gerstein and D. Oesterhelt and R. Henderson},
  title = {Electron Diffraction Analysis of Structural Changes in the Photocycle
	of Bacteriorhodopsin},
  journal = EMBO,
  year = {1993},
  volume = {12},
  pages = {1--8}
}

@ARTICLE{Sun93,
  author = {S. Sun},
  title = {Reduced Representation Model of Protein Structure Prediction: Statistical
	Potential and Genetic Algorithms},
  journal = {Protein Sci.},
  year = {1993},
  volume = {2},
  pages = {762--785}
}

@ARTICLE{Suzu93,
  author = {M. Suzuki},
  title = {Improved {T}rotter-like formula},
  journal = {Physics Letters A},
  year = {1993},
  volume = {180},
  number = {3},
  nremark = {(only articles relating to mathematical and theoretical methods in
	physics)}
}

@ARTICLE{SVOB93,
  author = {K. Svoboda and C.F. Schmidt and B.J. Schnapp and S.M. Block},
  title = {Direct observation of kinesin stepping by optical trapping interferometry},
  journal = NAT,
  year = {1993},
  volume = {365},
  pages = {721--727}
}

@ARTICLE{TAKE93,
  author = {H. Takei and A. Lewis},
  title = {Biphasic-{M} Decay of High {pH} Dehydrated Purple Membrane Studied
	with {Fourier} Transform Infrared Spectroscopy -- A Model Accounting
	for Functional Differences between Different {M}-Forms.},
  journal = PCPB,
  year = {1993},
  volume = {57},
  pages = {707--713}
}

@ARTICLE{TIRI93,
  author = {M. M. Tirion and D. {ben-Avraham}},
  title = {Normal Mode Analysis of {G}-Actin},
  journal = JMB,
  year = {1993},
  volume = {230},
  pages = {186--195}
}

@ARTICLE{ToMK93,
  author = {Douglas J. Tobia and Glenn J. Martyna and Michael L. Klein},
  title = {Molecular dynamics simulations of a protein in the canonical ensemble},
  journal = {J. Phys. Chem.},
  year = {1993},
  volume = {97},
  pages = {12959--12966},
  number = {49}
}

@ARTICLE{Toxv93,
  author = {S.~Toxvaerd},
  title = {Comment on: Reversible multiple time scale molecular dynamics},
  journal = JCP,
  year = {1993},
  volume = {99},
  pages = {2277}
}

@ARTICLE{Toxv93b,
  author = {S. Toxvaerd},
  title = {Molecular Dynamics at Constant Temperature and Pressure},
  journal = {Phys.\ Rev.\ E},
  year = {1993},
  volume = {47},
  pages = {343--350},
  number = {1},
  nremark = {Q 530.5 PR8XS}
}

@BOOK{TRAV93,
  title = {{DNA}-protein interactions},
  publisher = {Chapman \& Hall},
  year = {1993},
  author = {A. A. Travers},
  address = {London, New York}
}

@ARTICLE{TSAO93,
  author = {Y.-H. Tsao and D. F. Evans and H. Wennerstr$\ddot{o}$m},
  title = {Long-range attractive force between hydrophobic surfaces observed
	by atomic force microscopy},
  journal = SCI,
  year = {1993},
  volume = {262},
  pages = {547--550}
}

@ARTICLE{TuBM93,
  author = {M.~Tuckerman and B.~J.~Berne and G.~J.~Martyna},
  title = {Reply to comment on: Reversible multiple time scale molecular dynamics},
  journal = JCP,
  year = {1993},
  volume = {99},
  pages = {2278--2279}
}

@ARTICLE{TURN93,
  author = {G. J. Turner and L. J. W. Miercke and T. E. Thorgeirsson and D. S.
	Kliger and M. C. Betlach and R. M. Stroud},
  title = {Bacteriorhodopsin {D85N}: Three Spectroscopic Species in Equilibrium},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {1332--1337}
}

@INCOLLECTION{TWCL93,
  author = {J. D. Turner and P. K. Weiner and H. M. Chun and V. Lupi and S. Gallion
	and U. C. Singh},
  title = {Ch.\ 24},
  booktitle = {Computer Simulation of Biomolecular Systems: Theoretical and Experimental
	Applications},
  publisher = {ESCOM},
  year = {1993},
  editor = {W. F. Gunsteren and P. K. Weiner and A. J. Wilkinson},
  volume = {2},
  address = {Leiden}
}

@ARTICLE{WETE93,
  author = {M. {Van de Wetering} and M. Oosterwegel and K. van Norren and H.
	Clevers},
  title = {{SOX-4}, an {SRY}-like {HMG} box protein, is a transcriptional activator
	in lymphocytes},
  journal = EMBO,
  year = {1993},
  volume = {12},
  pages = {3847--54},
  number = {10}
}

@ARTICLE{VENA93,
  author = {R. M. Venable and Y. Zhang and B. J. Hardy and R. W. Pastor},
  title = {Molecular Dynamics Simulations of a lipid bilayer and of hexadeca
	ne: an investigation of membrane fluidity},
  journal = SCI,
  year = {1993},
  volume = {262},
  pages = {223--226}
}

@ARTICLE{VLIE93,
  author = {P.~C.~van der Vliet and C.~P.~Verrijzer},
  title = {Bending of {DNA} by Transcription Factors},
  journal = {BioEssays},
  year = {1993},
  volume = {15},
  pages = {25--32},
  number = {1},
  annote = {the gives a summary of how bending is determined experimentally and
	what the angles mean,mentions that effect of crystal packing on bending
	is not known, also gives a list of receptors that are known to bend
	DNA}
}

@ARTICLE{Wade93,
  author = {R.~C.~Wade and M.~E.~Davis and B.~A.~Luty and J.~D.~Madura and J.~A.~McCammon},
  title = {Gating of the active site of triose phosphate isomerase:Brownian
	dynamics simulations of flexible peptide loops in the enzyme},
  journal = BJ,
  year = {1993},
  volume = {64},
  pages = {9-15}
}

@ARTICLE{WaLe93,
  author = {Wahnstroem, G. and L.J. Lewis},
  title = {Molecular dynamics simulation of a molecular glass at intermediate
	times},
  journal = {PHYSICA A (Statistical and Theoretical Physics)},
  year = {1993},
  volume = {201},
  pages = {150},
  number = {Nos.~1, 2 and 3},
  nremark = {Proceedings of the International Workshop on Dynamics of Disordered
	Materials II, held in Grenoble, France on March 22 - 24, 1993 CHAPTER
	4. COMPUTER SIMULATION}
}

@ARTICLE{WALT93,
  author = {J\"org A. Walter and Klaus Schulten},
  title = {Implementation of Self-Organizing Neural Networks for Visuo-Motor
	Control of an Industrial Robot},
  journal = IEEENN,
  year = {1993},
  volume = {4},
  pages = {86--95},
  number = {1},
  annote = {Jan 1, 1993},
  tbtechrep = {TB-91-21}
}

@ARTICLE{WANG87A,
  author = {C.K. Wang and R. Liao and H.C. Cheung},
  title = {Rotational dynamics of skeletal muscle troponin {C}},
  journal = {J. Biol. Chem.},
  year = {1993},
  volume = {268},
  pages = {14671--7}
}

@ARTICLE{WANG93A,
  author = {K. Wang and R. McCarter and J. Wright and J. Beverly and R. Ramirez-Mitchell},
  title = {Viscoelasticity of the sarcomere matrix of skeletal muscles},
  journal = BJ,
  year = {1993},
  volume = {64},
  pages = {1161--1177}
}

@ARTICLE{WANG93,
  author = {N. Wang and J. P. Butler and D. E. Ingber},
  title = {Mechanotransduction Across the Cell Surface and Through the Cytoskeleton},
  journal = SCI,
  year = {1993},
  volume = {260},
  pages = {1124--1127}
}

@ARTICLE{WaKa93,
  author = {M. Watanabe and M. Karplus},
  title = {Dynamics of Molecules With Internal Degrees of Freedom by Multiple
	Time-Step Methods},
  journal = {J. Chem.\ Phys.},
  year = {1993},
  volume = {99},
  pages = {8063--8074},
  number = {10},
  nabstract = {In molecular dynamics simulations of flexible molecules, the treatment
	of motions that take place on different time scales (e.g., bond stretching
	and bond angle bending vs dihedral angle librations and overall translation
	and rotation) or of forces that vary differently with distance (e.g.,
	bonding forces vs electrostatic forces) is a major consideration.
	The most rapidly varying quantity limits the integration time step,
	while the most slowly varying quantity usually determines the simulation
	time required. The reversible multiple time-step methods introduced
	by Tuckerman, Berne, and Martyna, J. Chem. Phys. 97, 1990 (1992)
	allow one to use different integration time steps in the same simulation
	so as to treat the time development of the slow and fast motions
	most effectively. As a first step toward extending multiple time-step
	methods to macromolecules, we investigate their utility for determining
	the dynamics of n-alkanes as neat liquids and in aqueous solution.
	Because the dynamics is done in Cartesian rather than internal coordinates,
	the different time steps are implemented in terms of hard and soft
	forces acting on individual atoms; e.g., hard forces are contributed
	by bond stretching (and bond angle bending) terms and soft forces
	by the remaining intramolecular and intermolecular (van der Waals
	and electrostatic) terms in the additive empirical potential function
	used to describe these systems. Integrations with and without a Nose-Hoover
	thermostat are performed. Comparisons are made with ordinary single
	time step molecular dynamics and dynamics with constraints applied
	to the bonds. The stability of the integration methods and the dynamic
	properties are considered. It is shown that stable integrations that
	yield agreement with standard dynamics can be achieved with a saving
	of up to a factor of 5 in computer time.}
}

@ARTICLE{WATA93,
  author = {M.~Watanabe and M.~Karplus},
  title = {Dynamics of molecules with internal degrees of freedom by multiple
	time-step methods },
  journal = JCP,
  year = {1993},
  volume = {99},
  pages = {8063--8074},
  number = {10}
}

@ARTICLE{WEID93,
  author = {O.~Weidlich and F.~Siebert},
  title = {Time-resolved step-scan {FT-IR} investigations of the transition
	from {KL} to {L} in the bacteriorhodopsin photocycle: identification
	of chromophore twists by assigning hydrogen-out-of-plane {(HOOP)}
	bending vibrations},
  journal = AS,
  year = {1993},
  volume = {47},
  pages = {1394--1400}
}

@ARTICLE{WEIR93,
  author = {H. M. Weir and P. J. Kraulis and C. S. Hill and A. R. C. Raine and
	E. D. Laue and J. O. Thomas},
  title = {Structure of the {HMG} box motif in the {B}-domain of {HMG1}},
  journal = EMBO,
  year = {1993},
  volume = {12},
  pages = {1311--1319},
  number = {4}
}

@ARTICLE{WERN93,
  author = {U. Werner and W. Kuehnle and H. Staerk},
  title = {Magnetic field dependent reaction yields from radical ion pairs linked
	by a partially rigid aliphatic chain},
  journal = {J.~Phys.~Chem.},
  year = {1993},
  volume = {97},
  pages = {9280--9287}
}

@BOOK{WEST93,
  title = {Water and biological macromolecules},
  publisher = {CRC Press Inc.},
  year = {1993},
  author = {E. Westhof},
  address = {Boca Raton, Florida}
}

@ARTICLE{WILT93,
  author = {W. Wiltschko and U. Munro and H. Ford and R. Wiltschko},
  title = {Magnetic inclination compass: a basis for the migratory orientation
	of birds from the northern and southern hemisphere},
  journal = {Experentia},
  year = {1993},
  volume = {49},
  pages = {167--170}
}

@ARTICLE{WILT93A,
  author = {W. Wiltschko and U. Munro and H. Ford and R. Wiltschko},
  title = {Red light disrupts magnetic orientation of migratory birds},
  journal = NAT,
  year = {1993},
  volume = {364},
  pages = {525--527}
}

@ARTICLE{YoDP93,
  author = {Darrin M. York and Tom A. Darden and Lee G. Pedersen},
  title = {The effect of long-range electrostatic interactions in simulations
	of macromolecular crystals: A comparison of the {E}wald and truncated
	list methods},
  journal = {J. Chem.\ Phys.},
  year = {1993},
  volume = {99},
  pages = {8345--8348},
  number = {10}
}

@ARTICLE{Yosh93,
  author = {H.\ Yoshida},
  title = {Recent progress in the theory and application of symplectic integrators},
  journal = {Celest.\ Mech.\ Dynam.\ Astron.},
  year = {1993},
  volume = {56},
  pages = {27--43},
  nremark = {perturbed {H}amiltonian idea; see also Yosh90}
}

@ARTICLE{ZANE93,
  author = {M. Zanetti and G. Filaci and R.H. Lee and P. del Guercio and F. Rossi
	and R. Bacchetta and F. Stevenson and V. Barnaba and R. Billetta},
  title = {Expression of conformationally constrained adhesion peptide in an
	antibody {C}{D}{R} loop and inhibition of natural killer cell cytotoxic
	activity by an antibody antigenized with the {R}{G}{D} motif.},
  journal = {EMBO J.},
  year = {1993},
  volume = {12},
  pages = {4375--4384}
}

@ARTICLE{ZhSc93,
  author = {G. Zhang and T. Schlick},
  title = {{LIN}: A New Algorithm to Simulate the Dynamics of Biomolecules by
	Combining Implicit-Integration and Normal Mode Techniques},
  journal = JCC,
  year = {1993},
  volume = {14},
  pages = {1212--1233}
}

@ARTICLE{ZHAN93A,
  author = {X-k.~Zhang and M.~Pfahl},
  title = {Regulation of retinoid and thyroid hormone action through homodimeric
	and heterodimeric receptors.},
  journal = TEM,
  year = {1993},
  volume = {4},
  pages = {10--16}
}

@ARTICLE{ZHAN93B,
  author = {Y.N. Zhang and M.A. El-Sayed and M.L. Bonet and J.K. Lanyi and M.
	Chang and B. Ni and R. Needleman},
  title = { Effects of Genetic Replacements of Charged and {H}-Bonding Residues
	in the Retinal Pocket on {C}a$^{2+}$ Binding to Deionized Bacteriorhodopsin},
  journal = PNAS,
  year = {1993},
  volume = {90},
  pages = {1445--1449}
}

@ARTICLE{ZHOU93,
  author = {Feng Zhou and Andreas Windemuth and Klaus Schulten},
  title = {Molecular Dynamics Study of the Proton Pump Cycle of Bacteriorhodopsin},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {2291--2306},
  number = {9},
  tbtechrep = {TB-92-02}
}

@ARTICLE{ZhQi93,
  author = {W. J. Zhu and M. Z. Qin},
  title = {order conditions of 2 kinds of canonical difference schemes},
  journal = {COMPUTERS-\&-MATHEMATICS-WITH-APPLICATIONS},
  year = {1993},
  volume = {25},
  pages = {61--74},
  number = {6}
}

@ARTICLE{ZHU93,
  author = {Y. Zhu and R. Liu},
  title = {Divergent Pathways in Photobleaching of 7,9-{\it dicis}-Rhodopsin
	and 9,11-{\it dicis}-Fluororhodopsin: One-Photon-Two-Bond and One-Photon-One-Bond
	Isomerization},
  journal = BCH,
  year = {1993},
  volume = {32},
  pages = {10233--10238}
}

@INPROCEEDINGS{ZUBE93,
  author = {H. Zuber},
  title = {Structural features of photosynthetic light-harvesting systems},
  booktitle = {The Photosynthetic Reaction Center},
  year = {1993},
  editor = {J. Deisenhofer and J. R. Norris},
  pages = {43--100},
  address = {San Diego},
  publisher = {Academic Press}
}

@INPROCEEDINGS{WARR92,
  author = {Michael S. Warren and John K. Salmon},
  title = {Astrophysical {N}-body Simulations Using Hierarchical Tree Data Structures},
  booktitle = {Supercomputing~'92},
  year = {1992},
  pages = {570--576},
  month = NOV,
  publisher = {IEEE Computer Society Press},
  annote = {Livermore Loop defines: 1 SQRT = 4 FLOP, 1 division = 4 FLOP, 1 comparision
	= 1 FLOP}
}

@INPROCEEDINGS{WaSa92,
  author = {Michael S. Warren and John K. Salmon},
  title = {Astrophysical {N}-body Simulations Using Hierarchical Tree Data Structures},
  booktitle = {Supercomputing~'92},
  year = {1992},
  pages = {570--576},
  month = NOV,
  publisher = {IEEE Computer Society Press},
  nremark = {Livermore Loop defines: 1 SQRT = 4 FLOP, 1 division = 4 FLOP, 1 comparision
	= 1 FLOP}
}

@INPROCEEDINGS{CHCR92,
  author = {T.~W. Clark and R.~van Hanxleden and J.~A. McCammon and L. Ridgway},
  title = {Parallelization Strategies for a Molecular Dynamics Program},
  booktitle = {Intel Technology Focys Conference Oroceedings},
  year = {1992},
  month = APR
}

@INPROCEEDINGS{SAYL92,
  author = {R. Sayle and A. Bissel},
  title = {RasMol: A program for fast realistic rendering of molecular structures
	with shadows},
  booktitle = {Proceedings of the 10th Eurographics UK '92 Conference},
  year = {1992},
  month = APR
}

@TECHREPORT{STAM92,
  author = {Darrell C. Stam},
  title = {Distributed Homotopy Continuation and Its Application to Robotic
	Grasping},
  institution = {Beckman Institute},
  year = {1992},
  number = {UIUC-BI-AI-RCV-92-03},
  month = APR,
  annote = {about work Helmut Heller did with Darrell on the Transputers}
}

@ARTICLE{DEVO92,
  author = {Abraham M. {de\,Vos} and Mark Ultsch and Anthony A. Kossiakoff},
  title = {Human Growth Hormone and Extracellular Domain of its Receptor: Crystal
	Structure of the Complex},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {306--312}
}

@ARTICLE{Ader92,
  author = {Alan Aderem},
  title = {Signal Transduction and the Actin Cytoskeleton: The Roles of MARCKS
	and Profilin},
  journal = TIBS,
  year = {1992},
  volume = {17},
  pages = {438--443}
}

@ARTICLE{ALBE92,
  author = {A. Albeck and N. Livnah and H. Gottlieb and M. Sheves},
  title = {C$_{13}$ {NMR}-Studies of Model Compounds for Bacteriorhodopsin\
	--\ Facts Affecting the Retinal Chromophore Chemical-Shifts and Absorption
	Maximum},
  journal = JACS,
  year = {1992},
  volume = {114},
  pages = {2400--2411}
}

@ARTICLE{ALDE92,
  author = {R.G. Alden and M.C. Schneebeck and M.R. Ondrias and S.H. Courtney
	and J.M. Friedman},
  title = {Mode-Specific Relaxation Dynamics of Photoexcited {Fe(II)} Protoporphyrin
	{IX} in Hemoglobin},
  journal = {J.\ Raman Spectrosc.},
  year = {1992},
  volume = {23},
  pages = {569--574}
}

@ARTICLE{ALME92,
  author = {P.F.F. Almeida and W.L.C. Vaz and T.E. Thompson},
  title = {Lateral diffusion and percolation in two-phase, two component lipid
	bilayers. Topology of the solid-phase domains in-plane and across
	the lipid bilayer},
  journal = {Ann. N.Y. Acad. Sci.},
  year = {1992},
  volume = {31},
  pages = {7198--7210}
}

@ARTICLE{ALRO92,
  author = {I.~Alroy and L.~P.~Freedman},
  title = {{DNA} binding analysis of glucocorticoid receptor specificity mutants},
  journal = {Nucleic Acids Research},
  year = {1992},
  volume = {20},
  pages = {1045--1052},
  number = {5},
  annote = {compares the binding specificity of ER and GR, checks GLY,SER,VAL
	aa substitutions in particular ALA(ER)-not important vs VAL(GR)-important,
	the GLU(ER) is the discriminating aa, relies on GR-DNA cyrstal struct
	to compare results of specificity}
}

@ARTICLE{AMAT92,
  author = {Ivan Amato},
  title = {Molecular Design Gets Into a Hole},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {684},
  annote = {A bacterial toxin that self-assembles into cell-penetrating pores
	might give rise to new molecular technologies}
}

@ARTICLE{Ande92,
  author = {Christopher R. Anderson},
  title = {An Implementation of the Fast Multipole Method without Multipoles},
  journal = SJSSC,
  year = {1992},
  volume = {13},
  pages = {923--947},
  number = {4}
}

@INPROCEEDINGS{Ande04,
  author = {David P. Anderson},
  title = {BOINC: A System for Public-Resource Computing and Storage},
  booktitle = {5th IEEE/ACM International Workshop on Grid Computing},
  year = {2004},
  pages = {XX},
  address = {Pittsburg, USA},
  publisher = {IEEE/ACM}
}

@ARTICLE{ARCH92,
  author = {T.~K.~Archer and P.~Lefebvre and R.~G.~Wolford and G.~L.~Hager},
  title = {Transcription Factor Loading on the {MMTV} Promoter: A Bimodal Mechanism
	for Promoter Activation},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {1573--1576},
  annote = {refed in WOLF94, interferes? with GR activity}
}

@ARTICLE{BaCh92,
  author = {J. S. Bader and D. Chandler},
  title = {{C}omputer simulation study of the mean forces between ferrous and
	ferric ions in water},
  journal = {J. Phys. Chem.},
  year = {1992},
  volume = {96},
  pages = {6423}
}

@ARTICLE{BAIL92,
  author = {D.~H. Bailey},
  title = {How useful are Today's Parallel Computers?},
  journal = CIP,
  year = {1992},
  volume = {6},
  pages = {216},
  number = {2},
  annote = {Typical aerophysics programs get only 2% to 5% of the peak performance
	of CM2 or interl iPSC/860. Advocates FORTRAN90}
}

@ARTICLE{BAIR92,
  author = {A. Bairoch and B. Boeckmann},
  title = {The SWISS-PROT protein sequence data bank},
  journal = NAR,
  year = {1992},
  volume = {20},
  pages = {2019--2022}
}

@ARTICLE{BAMB92,
  author = {E. Bamberg and J. Tittor and D. Oesterhelt},
  title = {Light-Driven Proton or Chloride Pumping by Halorhodopsin},
  journal = PNAS,
  year = {1992},
  volume = {90},
  pages = {473--486}
}

@ARTICLE{BARB92,
  author = {G. Barbato and M. Ikura and L. E. Kay and R. W. Pastor and A. Bax},
  title = {Backbone Dynamics of Calmodulin Studied by $^{15}${N} Relaxation
	Using Inverse Detected Two-Dimensional {NMR} Spectroscopy: The Central
	Helix is Flexible},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {5269--5278}
}

@ARTICLE{BARN92,
  author = {Eric A. Barnard},
  title = {Receptor Classes and the Transmitter-Gated Ion Channels},
  journal = TIBS,
  year = {1992},
  volume = {17},
  pages = {368--374}
}

@ARTICLE{BARS92A,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten and Richard L.
	Magin},
  title = {Theory of Paramagnetic Contrast Agents in Liposome Systems},
  journal = MRM,
  year = {1992},
  volume = {24},
  pages = {1--13}
}

@ARTICLE{BARS92B,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten and J. Schoeniger
	and E. W. Hsu and S. Blackband},
  title = {Diffusional Edge Enhancement Observed by {NMR} in Thin Glass Capillaries},
  journal = CPL,
  year = {1992},
  volume = {200},
  pages = {88--96},
  tbtechrep = {TB-92-10}
}

@CONFERENCE{BARS92C,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten and J. S. Schoeniger
	and E. W. Hsu and Stephan J. Blackband},
  title = {Diffusional Edge Enhancement Observed by {NMR} Microscopy in Thin
	Glass Capillaries},
  booktitle = {Eleventh Annual Scientific Meeting and Exhibition, Works in Progress},
  year = {1992},
  publisher = {Society of Magnetic Resonance in Medicine, Inc.}
}

@ARTICLE{BASH92,
  author = {D. Bashford and K. Gerwert},
  title = {Electrostatic Calculations of the {pK} Values of Ionizable Groups
	in Bacteriorhodopsin},
  journal = {J. Mol. Biol.},
  year = {1992},
  volume = {224},
  pages = {473--486}
}

@ARTICLE{BaBS92,
  author = {D. Bassolino and R. E. Bruccoleri and S. Subramaniam},
  title = {Modeling the antigen combining site of an anti-dinitrophenol antibody},
  journal = {Prot. Sci.},
  year = {1992},
  volume = {1},
  pages = {1465}
}

@ARTICLE{BAUE91,
  author = {Wolfgang R. Bauer and Klaus Schulten},
  title = {Theory of Contrast Agents in Magnetic Resonance Imaging: Coupling
	of Spin Relaxation and Transport.},
  journal = MRM,
  year = {1992},
  volume = {26},
  pages = {16--39}
}

@ARTICLE{BAUE92,
  author = {Wolfgang R. Bauer and Klaus Schulten},
  title = {Nuclear Spin Dynamics {(I=1/2)} Under the Influence of Random Perturbation
	Fields in the ``Strong Collision'' Approximation},
  journal = BBG,
  year = {1992},
  volume = {96},
  pages = {721--727}
}

@ARTICLE{BEER92,
  author = {J.H. Beer and K.T. Springer and B.S. Coller},
  title = {Immobilized Arg-Gly-Asp ({R}{G}{D}) peptides of varying lengths as
	structural probes of the platelet glycoprotein {I}{I}b/{I}{I}{I}a
	receptor},
  journal = {Blood},
  year = {1992},
  volume = {79},
  pages = {117--128},
  number = {1}
}

@INCOLLECTION{BEKK92,
  author = {H. Bekker and E~J. Dijkstra and H.~J.~C. Berendsen},
  title = {Mapping molecular dynamics simulation calculations on a ring architecture},
  booktitle = {Parallel Computing: From Theory to Sound Practice},
  publisher = {{IOS} press},
  year = {1992},
  editor = {P. T. Wu and E. Milgrom},
  address = {Amsterdam},
  keywords = {task allocation; molecular dynamics; bandwidth reduction; ring architecture;
	SHAKE; REDUCE; parallel computation}
}

@ARTICLE{BELL92,
  author = {J.D. Bell and R.L. Biltonen},
  title = {Molecular details of the activation of soluble phospholipase {A$_2$}
	on lipid bilayers},
  journal = JBC,
  year = {1992},
  volume = {16},
  pages = {11046--11056}
}

@INPROCEEDINGS{BEREN92,
  author = {H. J. C. Berendsen and B. Egberts and S.-J. Marrink and P. Ahlstr{\"o}m},
  title = {Molecular dynamics simulation of phospholipid membranes and their
	interaction with phospholipase {A}$_2$. The Jerusalem Symposia on
	Quantum Chemistry and Biochemistry Vol. 25},
  booktitle = {Membrane proteins: Structures, interactions and models},
  year = {1992},
  editor = {A. Pullman, J. Jortner and B. Pullman},
  pages = {457--470},
  address = {Netherlands},
  publisher = {Kluwer Academic publishers},
  annote = {Mostly on membrane}
}

@ARTICLE{BERE92,
  author = {Alexander A. Berezin},
  title = {Correlated Isotopic Tunneling as a Possible Model for Consciousness},
  journal = JTB,
  year = {1992},
  volume = {154},
  pages = {415--420},
  annote = {sounds like total bullshit to me: no clear arguments, only whishi-whashi}
}

@ARTICLE{BeNe92,
  author = {B. A. Berg and T. Neuhaus},
  title = {Multicanonical Ensemble - a New Approach to Simulate 1st-Order Phase-Transitions},
  journal = PRL,
  year = {1992},
  volume = {68},
  pages = {9--12},
  abstract = {Relying on the recently proposed multicanonical algorithm, we present
	a numerical simulation of the first-order phase transition in the
	2D 10-state Potts model on lattices up to sizes 100 x 100. It is
	demonstrated that the new algorithm lacks an exponentially fast increase
	of the tunneling time between metastable states as a function of
	the linear size L of the system. Instead, the tunneling time diverges
	approximately proportional to L 2.65. On our largest lattice we gain
	more than 2 orders of magnitude as compared to a standard heat-bath
	algorithm. As a first physical application we report a high-precision
	computation of the interfacial free energy per unit area.},
  annote = {original multicanonical reference}
}

@ARTICLE{BIAN92,
  author = {M. E. Bianchi and L. Falciola and S. Ferrari and M. D.~J. Lilley},
  title = {The {DNA} binding site of {HMG1} protein is composed of two similar
	segments ({HMG} boxes), both of which have counterparts in other
	eukaryotic regulatory proteins},
  journal = EMBO,
  year = {1992},
  volume = {11},
  pages = {1055--1063},
  number = {3}
}

@ARTICLE{BLAS91A,
  author = {G. Blasdel},
  title = {Differential Imaging of Ocular Dominance and Orientation Selectivity
	in Monkey Striate Cortex},
  journal = {J. Neurosci.},
  year = {1992},
  volume = {12},
  pages = {3115},
  number = {8}
}

@ARTICLE{BLAS91B,
  author = {G. Blasdel},
  title = {Orientation Selectivity, Preference and Continuity in Monkey Striate
	Cortex},
  journal = {J. Neurosci.},
  year = {1992},
  volume = {12},
  pages = {3139},
  number = {8}
}

@BOOK{Blum92,
  title = {Software Engineering},
  publisher = {Oxford Univ.},
  year = {1992},
  author = {Bruce I. Blum},
  address = {New York}
}

@ARTICLE{BCLW92,
  author = {Board, Jr., John A. and J. W. Causey and Leathrum, Jr., James F.
	and Andreas Windemuth and Klaus Schulten},
  title = {Accelerated Molecular Dynamics Simulation with the Parallel Fast
	Multipole Algorithm},
  journal = {Chem.\ Phys.\ Lett.},
  year = {1992},
  volume = {198},
  pages = {89--94},
  nremark = {techrep TB-92-11}
}

@ARTICLE{BOAR92,
  author = {Board, Jr., John A. and J. W. Causey and Leathrum, Jr., James F.
	and Andreas Windemuth and Klaus Schulten},
  title = {Accelerated Molecular Dynamics Simulation with the Parallel Fast
	Multipole Algorithm},
  journal = CPL,
  year = {1992},
  volume = {198},
  pages = {89--94},
  tbtechrep = {TB-92-11}
}

@ARTICLE{BOHR92,
  author = {H. Bohr and R. Goldstein and P. G. Wolynes},
  title = {Predicting Surface Structures of Proteins by Neural Networks},
  journal = {Modelling, Measurement \& Control C31},
  year = {1992},
  volume = {55}
}

@ARTICLE{Brus92,
  author = {R.~Br\"{u}schweiler and B.~Roux and M.~Blackledge and C.~Griesinger
	and M.~Karplus and R.~R.~Ernst},
  title = {Influence of Rapid Intramolecular motion on NMR Cross-relaxation
	rates. A Molecular Dynamics study of Antanamide in solution},
  journal = JACS,
  year = {1992},
  volume = {114},
  pages = {2289--2302}
}

@ARTICLE{Bran92,
  author = {A. Brandt},
  title = {Multigrid methods in lattice field computations},
  journal = {Nucl. Phys. B (Proc. Suppl)},
  year = {1992},
  volume = {26},
  pages = {137--180}
}

@ARTICLE{BRAS92,
  author = {R. Brasseur and L. Lins and B. Vanloo and J.-M. Ruysschaert and M.
	Rosseneu},
  title = {Molecular Modeling of the Amphipathic Helices of the Plasma Apolipoproteins},
  journal = PRO,
  year = {1992},
  volume = {13},
  pages = {246--257}
}

@ARTICLE{BRES92,
  author = {E.~H.~Bresnick and M.~Bustin and V.~Marsaud and H.~Richard-Foy and
	G.~L.~Hager},
  title = {The transcriptionally-active {MMTV} promoter is depleted of histone
	{H1}},
  journal = NAR,
  year = {1992},
  volume = {20},
  pages = {273--278},
  annote = {disruption of H1 by hormone receptors}
}

@ARTICLE{BrHo92,
  author = {B.~R. Brooks and M. Hodo\u{s}\u{c}ek},
  title = {Parallelization of {CHARMM} for {MIMD} Machines},
  journal = CDA,
  year = {1992},
  volume = {7},
  pages = {16--22},
  number = {12},
  annote = {only reference so far for pCHARMm; keeps complete copy of all coords
	on each node (not usable for big systems); systems: intel Delat Touchstone,
	cluster of workstations; full CHARMm, but not all features are parallelized
	(actually only MD code is parallel); parallelizes bonded and nonbonded
	interactions; only very restricted version of SHAKE; method not completely
	scalable; all disk I/O is done from one node; on the CM5 the vectorization
	is very poor (runs in MIMD mode); uses cut-off; loss due to load
	balancing less than 10%; not atoms but pair interactions are distributed
	over the nodes (this is possible because all coords are on all nodes);
	no dynamic load balancing (said not to be necessary); uses a special
	devide and conquer communication scheme which uses a hypercube topology},
  keywords = {parallel CHARMm; molecular dynamics}
}

@ARTICLE{BROW92,
  author = {Michelle F. Browner and Eric B. Fauman and Robert J. Fletterick},
  title = {Tracking Conformational States in Allosteric Transitions of Phosphorylase},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {11297--11304}
}

@ARTICLE{BRYL92,
  author = {K. Bryl and M. Taiji and M. Yoshizava and T. Kobayashi},
  title = {Light Adaptation of Dark-adapted Bacteriorhodopsin Studied by Nanosecond
	Time-resolved Absorption Spectroscopy},
  journal = PCPB,
  year = {1992},
  volume = {56},
  pages = {1013--1018}
}

@ARTICLE{BRUN92,
  author = {Axel Br{\"u}nger},
  title = {The Free {R} Value: {A} Novel Statistical Quantity for Assessing
	the Accuracy of Crystal Structures},
  journal = NAT,
  year = {1992},
  volume = {355},
  pages = {472--474}
}

@BOOK{BRUN92a,
  title = {{X-PLOR}, Version~3.1: {A} System for {X}-ray Crystallography and
	{NMR}},
  publisher = {Yale University Press},
  year = {1992},
  author = {Axel T. Br{\"u}nger},
  address = {New Haven and London}
}

@INPROCEEDINGS{BARM92,
  author = {M. B{\"a}rmann and J. K{\"a}s and H. Kurzmeier and Erich Sackmann},
  title = {A New Cell Model --- Actin Networks Encaged by Giant Vesicles},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {137--143},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{CaSa92,
  author = {M. P. Calvo and J. M. Sanz-Serna},
  title = {Order conditions for canonical \mbox{Runge-Kutta-Nystr\"om} methods},
  journal = {BIT},
  year = {1992},
  volume = {32},
  pages = {131--142}
}

@INCOLLECTION{CAMP93b,
  author = {Tarcisio Campos and Klaus Schulten},
  title = {Learning Multiple Arm Postures of a Real Arm Robot},
  booktitle = {Intelligent Engineering Systems Through Artificial Neural Networks,
	{ANNIE-92}},
  publisher = {ASME Press},
  year = {1992},
  editor = {L. I. Burke and Y. C. Shin and C. H. Dagli},
  volume = {2},
  pages = {797--802},
  address = {New York},
  annote = {Although this has been published, we do not wish to include it in
	the main list of publications.}
}

@ARTICLE{CECK92,
  author = {Toni L. Ceckler and Steven D. Wolff and Virginia Yip and Sidney A.
	Simon and Robert S. Balaban},
  title = {Dynamics and Chemical Factors Affecting Water Proton Relaxation by
	Macromolecules},
  journal = JMR,
  year = {1992},
  volume = {98},
  pages = {637--645},
  annote = {this is an MRI paper, no real info on membranes}
}

@ARTICLE{CHAC92,
  author = {C. Chachaty and T. Bredel},
  title = {Nuclear Spin Relaxation and Dynamical Behaviour of Short-Chain Surfactants
	in Micellar and Liquid- Crystalline Aggregates},
  journal = JCS # { - Faraday Transactions},
  year = {1992},
  volume = {88},
  pages = {1893--1900},
  number = {13},
  address = {C Chachaty, Cens, Dept Rech Etat Condense, Drecam, SCM, BP 121, F-91191
	Gif sur Yvette, France},
  annote = {requested Tx=19920901., at binding},
  keywords = {MAGNETIC-RESONANCE RELAXATION; CORRELATED INTERNAL MOTIONS; MODEL-FREE
	APPROACH; MOLECULAR-DYNAMICS; BILAYER-MEMBRANES; {NMR}; MACROMOLECULES;
	SIMULATION}
}

@ARTICLE{CHAN92,
  author = {I. Chandrasekhar and G.M. Clore and A. Szabo and A.M. Gronenborn
	and B.R. Brooks},
  title = {A 500\,ps molecular dynamics simulation study of interleukin-1$\beta$
	in water},
  journal = JMB,
  year = {1992},
  volume = {226},
  pages = {239--250}
}

@ARTICLE{CHIA92,
  author = {N. C. Chia and R. Mendelsohn},
  title = {{CH2} Wagging Modes of Unsaturated Acyl Chains as {IR} Probes of
	Conformational Order in Methyl Alkenoates and Phospholipid Bilayers},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {10543--10547},
  number = {25},
  abstract = {CH2 wagging progressions have been monitored in the IR spectra of
	a series of methyl alkenoate solid phases and diunsaturated phosphatidylcholine
	(PC) aqueous gel phases. The acyl chain structures are of the form
	CH3(CH2)mC=C(CH2)nCO(=O)CH3. Band assignments for each series are
	verified from dispersion curves constructed with the assumption that
	the n CH2 groups between the C=C and ester moieties are solely responsible
	for the observed progressions. The utility of the progression intensities
	as a marker of acyl chain conformational order in the phospholipids
	is established through studies of thermotropic phase transitions
	in 1,2-dinervonoyl phosphatidylcholine (DNPC), 1,2-dierucoylPC (DErPC),
	and 1,2-dielaidoylPC (DEPC). Finally, the thermotropic behavior of
	the wagging progression intensities in diunsaturated PC/cholesterol
	mixtures is compared with that in 1,2-dipalmitoylPC (DPPC)/cholesterol.
	The unsaturated PC's exhibit a response at 33 mol % cholesterol that
	differs from DPPC. In particular, the "liquid-ordered" phase present
	in DPPC/cholesterol is absent for the unsaturated phospholipids under
	similar conditions of temperature and sterol concentration and is
	replaced by a substantially more disordered state. Implications of
	these results for the structure of biological membranes are discussed.},
  address = {RUTGERS STATE UNIV,NEWARK COLL ARTS \& SCI,DEPT CHEM,73 WARREN ST,
	NEWARK, NJ, 07102. RUTGERS STATE UNIV,NEWARK COLL ARTS \& SCI,DEPT
	CHEM,73 WARREN ST, NEWARK, NJ, 07102.},
  annote = {requested Tx=19930123.},
  keywords = {transform-infrared-spectroscopy. cholesterol. membranes. transitions.
	disorder. mixtures.}
}

@INPROCEEDINGS{CHIU92,
  author = {S.-W. Chiu and K. Gulukota and E. Jacobsson},
  title = {computational approaches in understanding the ion channel-lipid system},
  booktitle = {Membrane proteins: structures, interactions and models},
  year = {1992},
  editor = {A. Pullman},
  pages = {315--337},
  address = {Netherlands},
  publisher = {Kluwer Academic publishers}
}

@ARTICLE{CHOM92,
  author = {Christin T. Choma and Patrick T. T. Wong},
  title = {The structure of anhydrous and hydrated dimyristoylphosphatidyl glycerol:
	a pressure tuning infrared spectroscopic study},
  journal = CPLI,
  year = {1992},
  volume = {61},
  pages = {131--137},
  annote = {experimental work; good introduction; gives measurements for O-H,
	PO2-, C=O, CH2 bond stretching frequencies which could be compared
	to our simulations: frequency shifts indicate strength of hydrogen
	bonding},
  keywords = {hydrogen bonds},
  suggestions = {compare bond stretching frequencies of O-H, PO2-, C=O, CH2 with our
	simulations}
}

@ARTICLE{CHOU92,
  author = {K. C. Chou and L. Carlacci and G. M. Maggiora and L. A. Parodi and
	M. W. Shulz},
  title = {An Energy-based Approach to packing the 7-helix bundle of Bacteriorhodopsin},
  journal = {Protein Science},
  year = {1992},
  volume = {1},
  pages = {810--827}
}

@BOOK{Chui92,
  title = {An introduction to wavelets},
  publisher = {Academic Press},
  year = {1992},
  author = {C. K. Chui},
  address = {Boston}
}

@ARTICLE{CLAD92,
  author = {J. Cladera and M. Sab{\'e}s and E. Padr{\'o}s},
  title = {{Fourier} Transform Infrared Analysis of Bacteriorhodopsin Secondary
	Structure},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {12363--12368}
}

@INPROCEEDINGS{ClMS92,
  author = {Terry W. Clark and J. Andrew McCammon and L. Ridgway Scott},
  title = {Parallel Molecular Dynamics},
  booktitle = {Proceedings of the Fifth SIAM Conference on Parallel Processing for
	Scientific Computing},
  year = {1992},
  pages = {338--344},
  nremark = {Houston, Texas, March 1992}
}

@ARTICLE{COGD92,
  author = {R. J. Cogdell and P. O. Andersson and T. Gillbro},
  title = {Carotenoid singlet states and their involvement in photosynthetic
	light-harvesting pigments},
  journal = JPPB,
  year = {1992},
  volume = {15},
  pages = {105--112}
}

@ARTICLE{Cove92,
  author = {D. Covell},
  title = {Folding Protein Alpha-carbon Chains into Compact Forms by {M}onte
	{C}arlo Methods},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1992},
  volume = {14},
  pages = {192--204}
}

@ARTICLE{COWA92,
  author = {S. W. Cowan and T. Schirmer and G. Rummel and M. Steiert and R. Ghosh
	and R. A. Pauptit and J. N. Jansonius and J. P. Rosenbusch},
  title = {Crystal Structures Explain Functional Properties of 2 E. coli Porins},
  journal = NAT,
  year = {1992},
  pages = {727--733},
  number = {6389},
  address = {JN Jansonius, Univ Basel, Bioctr, Dept Struct Biol, CH-4056 Basel,
	Switzerland},
  annote = {requested Tx=19920925.},
  keywords = {PHOTOSYNTHETIC REACTION CENTER; INTEGRAL MEMBRANE- PROTEIN; ESCHERICHIA-COLI;
	OUTER-MEMBRANE; MACROMOLECULAR CRYSTALLOGRAPHY; RHODOPSEUDOMONAS-
	VIRIDIS; RHODOBACTER-CAPSULATUS; ELECTRON-MICROSCOPY; BACTERIAL PORIN;
	PHOE PORIN},
  publisher = {Macmillan Press Ltd, Brunel Rd, Houndmills, Basingstoke RG21 2XS,
	Hampshir, United Kingdom},
  voulme = {358}
}

@ARTICLE{CRAM92,
  author = {C.J. Cramer and D.G. Truhlar},
  title = {{AM1}-{SM2} and {PM3-SM3} parameterized {SCF} solvation models for
	free energies in aqueous solution},
  journal = {J. Comput.-Aid. Mol. Des.},
  year = {1992},
  volume = {6},
  pages = {629--666},
  annote = {PO4- solvation free energy}
}

@ARTICLE{CREU92,
  author = {Carl E. Creutz},
  title = {The Annexins and Exocytosis},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {924--931}
}

@ARTICLE{CROF92,
  author = {A. R. Crofts and B. Hacker and B. Barquera and C-H. Yun and R. B.
	Gennis},
  title = {Structure and function of the $bc$-complex of {{\em {R}hodobacter
	sphaeroides}}},
  journal = BBA,
  year = {1992},
  volume = {1101},
  pages = {162--165}
}

@ARTICLE{CRUZ92,
  author = {Carolina Cruz-Neira and Dan J. Sandin and Thomas A. DeFanti and R.
	V. Kenyon and J. C. Hart},
  title = {The {CAVE}: Audio Visual Experience Automatic Virtual Environment},
  journal = CACM,
  year = {1992},
  volume = {35},
  pages = {65--72}
}

@ARTICLE{DAMO92,
  author = {K. V. Damodaran and {Merz, Jr.}, Kenneth M. and Bruce Paul Gaber},
  title = {Structure and Dynamics of the Dilauroylphosphatidylethanolamine Lipid
	Bilayer},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {7656--7664},
  annote = {200ps; 1.5fs=dt; 48 lipids; 553 waters; periodic boundary; 41ps equilibration;
	cut-off=10\AA; coords saved every 10 steps; T=315K; here, too, order
	params for C1--C3 differ from experimental results; 15 waters solvating
	each lipid; water nead head groups less mobile than bulk water; gel
	phase has all-trans chains; LC phase is physiological one; short
	overview over experimental techniques: X-ray, neutron diffraction,
	{NMR}; interdigitation of about 4\AA; they have legends in their
	figures; CRAY-YMP},
  keywords = {simulation; DLPE; LC phase; order params; electron desity profiles;
	water pair distribution functions; velocity autocorrelation functions},
  suggestions = {make histogram of dihedral angles to estimate trans/gauche ratio;
	compute radial distribution functions for water; compute diffusion
	constant for water and look at differences bound water/ bulk water;
	compare 1-D diffusion of lipid in X and Z direction and look for
	differences}
}

@INPROCEEDINGS{Daub92,
  author = {I. Daubechies},
  title = {Ten lectures on wavelets},
  booktitle = {CBMS-NSF regional Conf. Ser. in Appl. Math. SIAM},
  year = {1992},
  address = {Philadelphia}
}

@ARTICLE{DERI92,
  author = {A. Deriu},
  title = {The Power of Quasielectric Neutron Scattering to Probe Biophysical
	Systems},
  journal = PHYB,
  year = {1992},
  volume = {182},
  pages = {349--360},
  number = {4},
  abstract = {Neutron high-resolution spectroscopic studies of biomolecular dynamics
	have been pursued actively in the last decade due to the recognised
	role of the microscopic dynamics in determining the functional properties
	of many biomolecular assemblies. As a result of instrumental advances
	and progress in molecular dynamics simulations it is nowadays possible
	to describe quantitatively the complex low-frequency motions exhibited
	by biologically active systems. Some selected examples referring
	to different biopolymers and biological membranes will be illustrated.},
  address = {UNIV PARMA,DIPARTIMENTO FIS,VIALE SCI, I-43100 PARMA, ITALY.},
  annote = {requested Tx=19930206.},
  keywords = {molecular-dynamics. protein-dynamics. water. transition. hydration.
	DNA. conformation. simulation. myoglobin. membranes.}
}

@ARTICLE{DEVE92b,
  author = {A. M. T. J. Deveer and P. A. Franken and R. Dijkman and J. Meeldijk
	and M. R. Egmond and H. M. Verheij and R. Verger and G. H. de Haas},
  title = {Competitive inhibition of lipolytic enzymes. VII. The interaction
	of pancreatic phospholipase {A}$_2$ with micellar lipid/water interfaces
	of competetive inhibitors},
  journal = BBA,
  year = {1992},
  volume = {1125},
  pages = {73--81}
}

@ARTICLE{DEVE92a,
  author = {A. M. T. J. Deveer and A. T. den Ouden and M. Vincent and J. Gallay
	and R. Verger M. R. Egmond and H. M. Verheij and G. H. de Haas},
  title = {Competitive inhibition of lipolytic enzymes. VIII: inhibitor-induced
	aggregation of porcine pancreatic phospholipase {A}$_2$},
  journal = BBA,
  year = {1992},
  volume = {1126},
  pages = {95--104}
}

@ARTICLE{DEXH92,
  author = {S. L. Dexheimer and Q. Wang and L. A. Peteanu and W. T. Pollard and
	R. A. Mathies and C. V. Shank},
  title = {Femtosecond Impulsive Excitation of Nonstationary Vibrational States
	in Bacteriorhodopsin},
  journal = CPL,
  year = {1992},
  volume = {188},
  pages = {61--66}
}

@ARTICLE{DICK92,
  author = {R.~E.~Dickerson},
  title = {{DNA} Structure from {A} to {Z}},
  journal = ME,
  year = {1992},
  volume = {211},
  pages = {67--111},
  annote = {review of {DNA}structures}
}

@ARTICLE{DiKG92,
  author = {H.-Q. Ding and N. Karasawa and W.~A. {Goddard III}},
  title = {The reduced cell multipole method for coulomb interactions in periodic
	systems with million-atom unit cell},
  journal = CPL,
  year = {1992},
  volume = {196},
  pages = {6--10},
  number = {6}
}

@ARTICLE{DING92,
  author = {Colin Dingwall and Ronald Laskey},
  title = {The Nuclear Membrane},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {942--947}
}

@INPROCEEDINGS{DOLA92,
  author = {C. Dolainsky and T. K{\"o}chy and C. Naumann and T. Brumm and S.
	J. Johnson},
  title = {Structure and Dynamics of Planar and Spherical Supported Phospholipid
	Bilayers},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {34--39},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{DRAT92,
  author = {E. A. Dratz and L. L. Holte},
  title = {The Molecular Spring Model for the Function of Docosahexaenoic Acid
	(22:6$\omega$3) in Biological Membranes},
  journal = UNKNOWN,
  year = {1992},
  volume = UNKNOWN,
  annote = {A pre-pre-preprint, probably not submitted anywhere yet}
}

@ARTICLE{EaTr92,
  author = {David J.~D. Earn and Scott Tremaine},
  title = {Exact Numerical Studies of {H}amiltonian Maps: Interating Without
	Roundoff Error},
  journal = {Physica D},
  year = {1992},
  volume = {56},
  pages = {1--22}
}

@ARTICLE{EDHO92,
  author = {O. Edholm and A. M. Nyberg},
  title = {Cholesterol in model membranes. A molecular dynamics simulation},
  journal = BJ,
  year = {1992},
  volume = {63},
  pages = {1081--1089},
  annote = {Studies of cholesterol membrane modelling}
}

@INPROCEEDINGS{EICK92,
  author = {T. von Eicken and D. E. Culler and S. C. Goldstein and K. E. Schauser},
  title = {Active messages: {A} mechanism for integrated communication and computation},
  booktitle = {Proceedings of the International Symposium on Computer Architecture},
  year = {1992}
}

@ARTICLE{ELSA92,
  author = {M. A. El-Sayed},
  title = {On the Molecular Mechanisms of the Solar to Electric Energy Conversion
	by the Other Photosynthetic System in Nature, Bacteriorhodopsin},
  journal = ACR,
  year = {1992},
  volume = {25},
  pages = {279--286},
  number = {7},
  address = {M. A. Elsayed, Univ Calif Los Angeles, Dept Chem \& Biochem, Los
	Angeles, CA 90024},
  annote = {requested Tx=19920901.},
  keywords = {RESONANCE RAMAN-SPECTRA; INFRARED DIFFERENCE SPECTROSCOPY; DARK-ADAPTED
	BACTERIORHODOPSIN; CONTAINING MEMBRANE FRAGMENTS; ARTIFICIAL RETINAL
	ANALOGS; DRIVEN PROTONATION CHANGES; INTERNAL ASPARTIC ACIDS; LABELED
	PURPLE MEMBRANE; INDUCED volume CHANGES; PICOSECOND TIME SCALE}
}

@ARTICLE{ERIK92,
  author = {J. C. Eriksson and S. Ljunggren},
  title = {Is It Necessary That the Interfacial Tension of a General Curved
	Interface Is Constant Along the Interface at Equilibrium?},
  journal = JCIS,
  year = {1992},
  volume = {152},
  pages = {575--577},
  number = {2},
  address = {JC Eriksson, Royal Inst Technol, Dept Phys Chem, S-10044 Stockholm
	70, Sweden},
  annote = {requested Tx=19920925.},
  keywords = {SPHERICAL INTERFACE; SURFACE-TENSION; MICROEMULSIONS; MEMBRANES},
  publisher = {Academic Press, Inc, 1250 Sixth Ave, San Diego, CA 92101}
}

@ARTICLE{ERIK92A,
  author = {Mats A.~L.~Eriksson and Aattoo Laaksonen},
  title = {A Molecular Dynamics Study of Conformational Changes and Hydration
	of Left-Handed d({\sc CGCGCGCGCGCG}) in a Nonsalt Solution},
  journal = {Biopolymers},
  year = {1992},
  volume = {32},
  pages = {1035--1059},
  annote = {haven't read it yet, includes water in the simulation, is an excellent
	source of information on how to read and interprete dials and windows,
	a 70ps trajectory, has long discussion on solvation water bridges,
	only problem is that it's Z-DNA}
}

@INCOLLECTION{ERWI91A,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Formation of Dimension-Reducing Somatotopic Maps},
  booktitle = {Proceedings of the Fourth Conference on Neural Networks and Parallel
	Distributed Processing},
  publisher = {Indiana University at Fort Wayne},
  year = {1992},
  editor = {Samir I. Sayegh},
  pages = {115--126},
  annote = {The title of the lecture at the conference was ``Formation and Variability
	of Somatotopic Maps with Topological Mismatch'', but that is NOT
	the title of this article; the entry duplixcates ERWI92}
}

@INCOLLECTION{ERWI92,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Formation of Dimension-Reducing Somatotopic Maps},
  booktitle = {Proceedings of the Fourth Conference on Neural Networks and Parallel
	Distributed Processing},
  publisher = {Indiana University at Fort Wayne},
  year = {1992},
  editor = {Samir I. Sayegh},
  pages = {115--126},
  annote = {The title of the lecture at the conference was ``Formation and Variability
	of Somatotopic Maps with Topological Mismatch'', but that is NOT
	the title of this article.}
}

@ARTICLE{ERWI92A,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Self-Organizing Maps: Ordering, Convergence Properties and Energy
	Functions},
  journal = BC,
  year = {1992},
  volume = {67},
  pages = {47--55},
  number = {1},
  annote = {Technical report TB-91-11 combines two papers into one.},
  tbtechrep = {TB-91-11}
}

@ARTICLE{ERWI92B,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Self-Organizing Maps: Stationary States, Metastability and Convergence
	Rate},
  journal = BC,
  year = {1992},
  volume = {67},
  pages = {35--45},
  number = {1},
  annote = {Technical report TB-91-11 combines two papers into one.},
  tbtechrep = {TB-91-11}
}

@ARTICLE{ESTE92,
  author = {J.E. Estes and L.A. Selden and H.J. Kinosian and L.C. Gershman},
  title = {Tightly-bound divalent cation of actin},
  journal = JMRCM,
  year = {1992},
  volume = {13},
  pages = {272--284}
}

@ARTICLE{FAHM92,
  author = {K. Fahmy and O. Weidlich and M. Engelhard and J. Tittor and D. Oesterhelt
	and F. Siebert},
  title = {Identification of the Proton Acceptor of {Schiff} Base Deprotonation
	in Bacteriorhodopsin: A {Fourier}-Transform Infrared Study of the
	Mutant {Asp85}\,$\rightarrow$\,{Glu} in Its Natural Lipid Environment},
  journal = PCPB,
  year = {1992},
  volume = {56},
  pages = {1073--1083}
}

@ARTICLE{FAUP92,
  author = {P. Faupel and V. Buss},
  title = {Conformational Analysis and Electronic Structure Calculations of
	s-1,2-bis(2-dibutenoyl)glycerol and s-1,2-bis(2,4-hexadienoyl)glycerol,
	2~Analogues of 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphorylcholine},
  journal = MCTS,
  year = {1992},
  volume = {1},
  pages = {311--320},
  number = {5},
  abstract = {As a model for 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphorylcholine,
	a doubly unsaturated membrane-forming lipid molecule, force-field
	({MMP2}) calculations were performed on S-1,2-bis(2-dibutenoyl)glycerol,
	and CNDO/S-calculations b) on the derived minimum-energy conformations
	of S-1,2-bis(2,4-hexadienoyl)glycerol. The energy hypersurface especially
	with respect to the dihedral angles along the C(1)-C(2) and the two
	C-O ester bonds was explored and the rotational strength as a function
	of these angles was calculated. The two gauche-forms were found to
	be most stable, with a slight preference for the g--form. The experimental
	circular dichroism data obtained for 1,2-bis(2,4-hexadienoyl)-sn-glycero-3-phosphorylcholine,
	the corresponding phosphorylcholine, indicate a dynamic equilibrium
	between two forms of opposite chirality possibly involving the g+-
	and the g--forms.},
  address = {UNIV DUISBURG GESAMTHSCH,FACHGEBIET THEORET CHEM,LOTHARSTR 1, W-4100
	DUISBURG, GERMANY. UNIV DUISBURG GESAMTHSCH,FACHGEBIET THEORET CHEM,LOTHARSTR
	1, W-4100 DUISBURG, GERMANY.},
  annote = {requested Tx=19930123.},
  keywords = {phosphatidylethanolamine. phospholipids. packing. lipids.}
}

@ARTICLE{FERR92a,
  author = {S. Ferrari and V. R. Harley and A. Pontiggia and P. N. Goodfellow
	and R. Lovell-Badge and M. E. Bianchi},
  title = {{SRY}, like {HMG1}, recognizes sharp angles in {DNA}},
  journal = EMBO,
  year = {1992},
  volume = {11},
  pages = {4497--4506},
  number = {12}
}

@ARTICLE{FERR92,
  author = {A. Ferrarini and P. L. Nordio},
  title = {Diffusion Models for the Dynamics of Flexible Molecules},
  journal = JCS # { - Faraday Transactions},
  year = {1992},
  volume = {88},
  pages = {1733--1746},
  number = {13},
  address = {PL Nordio, Univ Padua, Dept Phys Chem, I-35131 Padua, Italy},
  annote = {requested Tx=19920901.},
  keywords = {SPIN-LATTICE-RELAXATION; ANISOTROPIC REORIENTATIONAL RELAXATION; UNIAXIAL
	LIQUID-CRYSTALS; KERR EFFECT MEASUREMENTS; PHOSPHOLIPID-MEMBRANES;
	{NMR} RELAXATION; BIPHENYL; BILAYER; DEPENDENCE; PHOTOISOMERIZATION}
}

@ARTICLE{FREE92,
  author = {L.~P.~Freedman},
  title = {Anatomy of the Steroid Receptor Zinc Finger Region},
  journal = {Endocrine Revs.},
  year = {1992},
  volume = {13},
  pages = {129--145},
  number = {2},
  annote = {see DIST93 also a good review}
}

@ARTICLE{FREY92,
  author = {W. Frey and Erich Sackmann},
  title = {Solitary Waves in Asymmetric Soap Films},
  journal = LM,
  year = {1992},
  volume = {8},
  pages = {3150--3154},
  number = {12},
  abstract = {We report hydrodynamic instabilities in thin lipid-water films on
	a hydrophilic solid substrate (asymmetric soap film), stabilized
	vertically and in contact to a film balance in a surrounding of saturated
	humidity. A solitary wave is generated by pushing a lipid monolayer
	onto the water film. The experimental data fit to a long wave expansion
	theory by including the Marangoni effect.},
  address = {TECH UNIV MUNICH,DEPT PHYS, W-8046 GARCHING, GERMANY. TECH UNIV MUNICH,DEPT
	PHYS, W-8046 GARCHING, GERMANY.},
  annote = {requested Tx=19930206.},
  keywords = {FINGERING-INSTABILITY}
}

@MANUAL{GAUS92,
  title = {Gaussian 92, Revision A},
  author = {M. J. Frisch and G. W. Trucks and M. Head-Gordon and P. M. W. Gill
	and M. W. Wong and J. B. Foresman and B. G. Johnson and H. B. Schlegel
	and M. A. Robb and E. S. Replogle and R. Gomperts and J. L. Andres
	and K. Raghavachari and J. S. Binkley and C. Gonzalez and R. L. Martin
	and D.~J. Fox and D.~J. Defrees and J. Baker and J. J. P. Stewart
	and J. A. Pople},
  organization = {Gaussian Inc.},
  address = {Pittsburgh, PA},
  year = {1992}
}

@ARTICLE{GAO92,
  author = {J. Gao and X. Xia},
  title = {A Priori Evaluation of Aqueous Polarization Effects Throug {M}onte
	{C}arlo {QM-MM} Simulations},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {631--635}
}

@ARTICLE{GAT92,
  author = {Y. Gat and M. Grossjean and I. Pinevsky and H. Takei and Z. Rothman
	and H. Sigrist and A. Lewis and M. Sheves},
  title = {Participation of Bacteriorhodopsin Active-Site Lysine Backbone in
	Vibrations Associated with Retinal Photochemistry},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {2434--2438}
}

@ARTICLE{GAWR92,
  author = {K. Gawrisch and D. Ruston and J. Zimmerberg and V.A. Parsegian and
	R.P. Rand and N. Fuller},
  title = {Membrane dipole potentials, hydration forces, and the ordering of
	water at membrane surfaces},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {1213--1223}
}

@ARTICLE{Gear92,
  author = {C.W. Gear},
  title = {Invariants and numerical methods for ODEs},
  journal = {Physica\ D},
  year = {1992},
  volume = {60},
  pages = {303--310}
}

@ARTICLE{GERW92,
  author = {K. Gerwert},
  title = {Molecular reaxtion mechanism of photosynthetic proteins as determined
	by {FTIR}-spectroscopy},
  journal = BBA,
  year = {1992},
  volume = {1101},
  pages = {147--153}
}

@ARTICLE{GFPV92,
  author = {Getzoff, E. D. and Fisher, C. L. and Page, H. E. and Viezzoli, M.
	S. and Banci, L. and Hallewell, R. A.},
  title = {Faster Superoxide Dismutase Mutants Designed by Enhancing Electrostatic
	Steering},
  journal = NAT,
  year = {1992},
  volume = {358},
  pages = {347}
}

@ARTICLE{GIES92,
  author = {K. Giese and J. Cox and R. Grosschedl},
  title = {The {HMG} box of Lymphoid Enhancer Factor 1 bends {DNA} and facilitates
	assembly of functional nucleoprotein structures},
  journal = {Cell},
  year = {1992},
  volume = {69},
  pages = {185--195}
}

@ARTICLE{GLAZ92,
  author = {James A. Glazier and Francois Graner},
  title = {Simulation of Biological Cell Sorting Using a Two-Dimenional Extended
	Potts Model},
  journal = {Physical Review Letters},
  year = {1992},
  volume = {69},
  pages = {2013--2016}
}

@ARTICLE{GOET92,
  author = {Barbara M. Goettgens and Ralf W. Tillmann and Manfred Radmacher and
	Hermann E. Gaub},
  title = {Molecular Order in Polymerizable Langmuir-Blodgett Films Probed by
	Microfluorescence and Scanning Force Microscopy},
  journal = LM,
  year = {1992},
  volume = {8},
  pages = {1768--1774},
  number = {7},
  address = {HE Gaub, Tech Univ Munich, Dept Phys, W-8046 Garching, Germany},
  annote = {not relevant for study of biological membranes; that is what I thought
	at first but now it seems i was COMPLETELY wrong!},
  keywords = {MULTILAYERS; MONOLAYERS; RESOLUTION; MEMBRANES}
}

@ARTICLE{Goldstein92,
  author = {RA Goldstein and ZA Luthey-Schulten and PG Wolynes},
  title = {Protein tertiary structure recognition using optimized {H}amiltonians
	with local interactions},
  journal = {Proc Natl Acad USA},
  year = {1992},
  volume = {89},
  pages = {9029--9033},
  comments = {This article talks about profile and contact Hamiltonians. See Word
	document with notes for this article.}
}

@ARTICLE{GOMP92,
  author = {G. Gompper and D. M. Kroll},
  title = {Inflated Vesicles --- A New Phase of Fluid Membranes},
  journal = EPL,
  year = {1992},
  volume = {19},
  pages = {581--586},
  number = {7},
  address = {G Gompper, Univ Munich, Sekt Phys, Theresienstr 37, W-8000 Munich
	2, Germany},
  annote = {requested Tx=19920925.},
  keywords = {Fluctuation Phenomena, Random Processes, and Brownian Motion; General
	Studies of Phase Transitions; Membrane Biophysics; TRIANGULATED RANDOM
	SURFACES; CRUMPLING TRANSITION; ELASTICITY; CURVATURE; SHAPES},
  publisher = {Editions Physique, Z I de Courtaboeuf Ave, Ave du Hoggar B-P 112,
	91944 les Ulis Cedex, France}
}

@BOOK{Good92,
  title = {The Machinery of Life},
  publisher = {Springer-Verlag},
  year = {1992},
  author = {David S. Goodsell},
  address = {New York},
  nremark = {574.87 G628m Biology --popularization--}
}

@ARTICLE{GOUD92,
  author = {H. Gouda and H. Torigoe and A. Saito and M. Sato and Y. Arata and
	I. Shimada},
  title = {Three-dimensional solution structure of the {B} domain of staphylococcal
	protein {A}: comparisons of the solution and crystal structures},
  journal = BC,
  year = {1992},
  volume = {31},
  pages = {9665}
}

@ARTICLE{GRAB92,
  author = {Z. Grabarek and T. Tao and J. Gergely},
  title = {Molecular Mechanism of Troponin {C} Function},
  journal = {J. Muscle Res. Cell Motil.},
  year = {1992},
  volume = {13},
  pages = {383--393}
}

@ARTICLE{GRAH92,
  author = {R. Graham and K. Freed},
  title = {{\it Ab Initio} Study of the {\it trans}-{Butadiene} {$\pi$}-{Valance}
	States Using the Effective Valence Shell Hamiltonian Method.},
  journal = JCP,
  year = {1992},
  volume = {96},
  pages = {1304--1316}
}

@ARTICLE{GrGl92,
  author = {F. Graner and J. A. Glazier},
  title = {Simulation of biological cell sorting using a two-dimensional extended
	Potts model},
  journal = PRL,
  year = {1992},
  volume = {69},
  pages = {2013--2016},
  number = {13}
}

@ARTICLE{GROS91,
  author = {M. K. Grossjean and Michael F. Grossjean and Klaus Schulten and Paul
	Tavan},
  title = {Semistochastic Approach to Many Electron Systems},
  journal = JCP,
  year = {1992},
  volume = {97},
  pages = {1865--1875},
  number = {3}
}

@ARTICLE{GROSS91,
  author = {M. K. Grossjean and Michael F. Grossjean and Klaus Schulten and Paul
	Tavan},
  title = {Semistochastic Approach to Many Electron Systems},
  journal = JCP,
  year = {1992},
  volume = {97},
  pages = {1865--1875},
  number = {3}
}

@ARTICLE{JHHA92,
  author = {J-H.~Ha and M.~W.~Capp and M.~D.~Hohenwalter and W.~Baskerville and
	M.~T.~Record},
  title = {Thermodynamic Stoichiometries of Participation of Water, Cations
	and Anions in Specific and Non-specific Binding of {\it lac} Repressor
	to {DNA}},
  journal = JMB,
  year = {1992},
  volume = {228},
  pages = {252--264},
  annote = {experimental study of binding related to various ions and concs.
	also subtitled "possible thermodynamic origins of the "glutamate
	effect" on protein--DNA interactions}
}

@BOOK{Hail92,
  title = {Molecular Dynamics Simulation},
  publisher = {John Wiley and Sons},
  year = {1992},
  author = {J. M. Haile}
}

@ARTICLE{HAMP92,
  author = {N. Hampp and C. Brauchle and D. Oesterhelt},
  title = {Mutated Bacteriorhodopsins --- Competitive Materials for Optical
	Information Processing},
  journal = MRB,
  year = {1992},
  volume = {17},
  pages = {56--60},
  number = {11},
  address = {UNIV MUNICH, W-8000 MUNICH 2, GERMANY},
  annote = {requested Tx=19921217.},
  keywords = {purple-membrane; correlator; rhodopsin; protein; crystal}
}

@ARTICLE{HANX92,
  author = {Reinhard v. Hanxleden and L. Ridgway Scott},
  title = {Correctness and determinism of Parallel {M}onte {C}arlo Processes},
  journal = PA,
  year = {1992},
  volume = {18},
  pages = {121--132},
  annote = {not very interesting}
}

@ARTICLE{HAO92,
  author = {M. Hao and S. Harvey},
  title = {Analyzing the Normal Mode Dynamics of Macromolecules by the Component
	Synthesis Method},
  journal = BP,
  year = {1992},
  volume = {32},
  pages = {1393}
}

@ARTICLE{HARL92,
  author = {V. R. Harley and D. I. Jackson and P. J. Hextall and J. R. Hawkins
	and G. D. Berkovitz and S. Sockanathan and R. Lovell-{B}adge and
	P. N. Goodfellow},
  title = {{DNA}-binding activity of recombinant {SRY} from normal males and
	{XY} females},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {453--456}
}

@ARTICLE{HEGI92,
  author = {L. Heginbotham and T. Abramson and R. Mac{K}innon},
  title = {A functional connection between the pores of distantly related ion
	channels as revealed by mutant {K}$^+$ channels},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {1152--1155},
  annote = {This is also about the selectivity filter}
}

@ARTICLE{HELL92B,
  author = {Helmut Heller and Klaus Schulten},
  title = {Parallel Distributed Computing for Molecular Dynamics: Simulation
	of Large Heterogeneous Systems on a Systolic Ring of Transputers},
  journal = CDA,
  year = {1992},
  volume = {7},
  pages = {11--22},
  number = {8},
  annote = {Also published in Proceedings of the Fifth Conference on Neural Networks
	and Distributed Parallel Processing, Indiana University--Purdue University
	at Fort Wayne, Samir I.\ Sayegh, Ed. pp. 55-76 (1992).},
  tbtechrep = {TB-92-09}
}

@ARTICLE{HEYN92,
  author = {M. P. Heyn and H. Otto},
  title = {Photoselection and Transient Linear Dichroism with Oriented Immobilized
	Purple Membranes: Evidence for Motion of the {C(20)}-methyl Group
	of the Chromophore towards the Cytoplasmic Side of the Membrane},
  journal = PCPB,
  year = {1992},
  volume = {56},
  pages = {1105--1112}
}

@BOOK{HILL92,
  title = {Ionic channels of excitable membranes},
  publisher = {Sinauer Associates},
  year = {1992},
  author = {B.~Hille.},
  address = {Sunderland, MA},
  edition = {2nd}
}

@INPROCEEDINGS{HIRO92,
  author = {Hirosawa, M. and Ishikawa, M.},
  title = {Temperature Parallel Simulated Annealing --- Application in Biological
	Problems.},
  booktitle = {Abstract: Workshop on High Performance Computing and Grand Challenges
	in Structural Biology},
  year = {1992},
  pages = {24--27},
  address = {Florida State University}
}

@ARTICLE{HIRS92,
  author = {M.~A.~Hirst and L.~Hinck and M.~Danielsen and G.~M.~Ringold},
  title = {Discrimination of {DNA} response elements for thyroid hormone and
	estrogen is dependent on dimerization of receptor {DNA}},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {5527--5531},
  annote = {locates the 5aa that distinquish ER from TR and relates to dimerization}
}

@ARTICLE{HoSa92,
  author = {L. Holm and C. Sander},
  title = {Fast and Simple {M}onte {C}arlo Algorithm for Side Chain Optimization
	in Proteins: Application to Model Building by Homology},
  journal = {Proteins: Struct., Funct., Genet.},
  year = {1992},
  volume = {14},
  pages = {213--223}
}

@ARTICLE{TAO92,
  author = {T.~Hsieh},
  title = {{DNA} topoisomerases},
  journal = COCB,
  year = {1992},
  volume = {4},
  pages = {396--400},
  annote = {two types of topo's typeI breaks and rejoins one strand, typeIIbreaks
	both strands and passes {DNA}across DNA, ie crosses strands it's
	a review that points to many others covers function topos in chromosome
	segregation,condensation, and struc and func analysis}
}

@ARTICLE{HUBE92,
  author = {R. Huber and R. Berendes and A. Burger},
  title = {Crystal and Molecular Structure of Human Annexin {V} after Refinement.
	{I}mplications for Structure, Membrane Binding and Ion Channel Formation
	of the Annexin Family of Proteins.},
  journal = JMB,
  year = {1992},
  volume = {223},
  pages = {683--704}
}

@ARTICLE{IKUR92,
  author = {Mitsuhiko Ikura and G. Marius Clore and Angela M. Gronenborn and
	Guang Zhu and Claude B. Klee and Ad Bax},
  title = {Solution Structure of a Calmodulin-Target Peptide Complex by Multidimensional
	{NMR}},
  journal = SCI,
  year = {1992},
  volume = {256},
  pages = {632--638}
}

@BOOK{ISRA92a,
  title = {Intermolecular and Surface Forces},
  publisher = {Academic Press},
  year = {1992},
  author = {J. N. Israelachvili},
  address = {London}
}

@ARTICLE{ISRA92,
  author = {Jacob N. Israelachvili and H{\aa}kan Wennerstr{\"o}m},
  title = {Entropic Forces between Amphiphilic Surfaces in Liquids},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {520--531},
  annote = {hydration force not due to water structure; additional strong repulsive
	short range (10\AA--30\AA) force; characteristic decay length is
	2\AA; surface tension water/POPC=53mN/m; pressure as derivative of
	free energy},
  keywords = {hydration force; DLVO-theorie; head groups},
  suggestions = {look at water structure: are there oscillations?}
}

@ARTICLE{JACO92,
  author = {Robert Jacob and John Anderson},
  title = {Do-it-Yourself Massively Parallel Supercomputer Does Useful Physics},
  journal = CIP,
  year = {1992},
  volume = {6},
  pages = {244--251},
  number = {3},
  annote = {references our MS article on Transputers; does a weather simulation:
	microbursts on their self built 204 T800 machine},
  keywords = {WME}
}

@ARTICLE{JAIN92,
  author = {Jain, A. and Vaidehi N. and Rodriguez G.},
  title = {A Fast Recursive Algorithm for Molecular Dynamics Simulations},
  journal = {J. of Comp. Phys.},
  year = {1992},
  note = {submitted}
}

@INCOLLECTION{JONA92,
  author = {Ana Jonas},
  title = {Lipid-Binding Properties of Apolipoproteins},
  booktitle = {Structure and Function of Apolipoproteins},
  publisher = {CRC Press, Inc.},
  year = {1992},
  editor = {Maryvonne Rosseneu},
  chapter = {8},
  address = {Boca Raton, Florida}
}

@ARTICLE{JoTT92,
  author = {D. Jones and W. Taylor and J. Thornton},
  title = {A New Approach to Protein Fold Recognition},
  journal = NAT,
  year = {1992},
  volume = {358},
  pages = {86--89}
}

@ARTICLE{KREM92,
  author = {Alexander K\v{r}emen},
  title = {Biological Molecular Energy Machines as Measuring Devices},
  journal = JTB,
  year = {1992},
  volume = {154},
  pages = {405--413},
  annote = {no real arguments but a lot of words; doesn't convince me}
}

@ARTICLE{KAHN92A,
  author = {T. W. Kahn and D. M. Engelman},
  title = {Bacteriorhodopsin Can Be Refolded from Two Independently Stable Transmembrane
	Helices and the Complementary Five-Helix Fragment},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {6144--6151}
}

@ARTICLE{KAHN92B,
  author = {T. W. Kahn and J. M. Sturtevant and D. M. Engelman},
  title = {Thermodynamic Measurements of the Contributions of Helix-Connecting
	Loops and of Retinal to the Stability of Bacteriorhodopsin},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {8829--8839}
}

@BOOK{KAMP92,
  title = {Stochastic Processes in Physics and Chemistry},
  publisher = {North-Holland},
  year = {1992},
  author = {N. G. van Kampen},
  address = {Amsterdam, New York}
}

@ARTICLE{KARA92,
  author = {S. Karaborni and S. Toxvaerd},
  title = {Tilt Transitions in Langmuir Monolayers of Long-chain Molecules},
  journal = JCP,
  year = {1992},
  volume = {32},
  number = {46},
  address = {SHELL INT RES MAATSCHAPPIJ BV,KONINKLIJKE SHELL LAB AMSTERDAM,POB
	3003, 1003 AA AMSTERDAM, NETHERLANDS. HC ORSTED INST,DEPT CHEM, DK-2100
	COPENHAGEN 0, DENMARK},
  annote = {Molecular dynamics simulations have been used to investigate tilt
	transitions in a monolayer model of amphiphilic molecules at an air-water
	interface. Eight simulations were performed at 300 K on monolayers
	in the density range of 18.5-25 angstrom2/molecule. The model amphiphilic
	molecules contained 19 pseudoatoms, each representing a methyl or
	a methylene group, and a head group representing a carboxylate group.
	Amphiphile-amphiphile interactions were modeled using a new anisotropic
	united atom model that accounts implicitly for the presence of hydrogen
	atoms in alkanes; water-amphiphile interactions were modeled using
	two external potentials that do not constrain the head groups to
	the interface, allow methylene segments to enter the water, and provide
	a finite size interface of the same order of magnitude as the size
	of the experimental water-air interface. The tilt behavior of the
	monolayer was monitored as a function of molecular area. Tilt angle
	results and structure factor analysis point to the occurrence of
	a transition between 20 and 21 angstrom2/molecule from an almost
	upright to a tilted monolayer. At 21 and 22 angstrom2/molecule, the
	monolayers do not have a well-defined tilt order. Upon monolayer
	expansion to 23 angstrom2/molecule, the molecules become tilted over
	their nearest neighbors.; requested Tx=19921125.},
  keywords = {AIR-WATER-INTERFACE; X-RAY-REFLECTIVITY; DYNAMICS-SIMULATIONS; FATTY-ACIDS;
	BILAYER-MEMBRANE; ETHYL-ESTERS; PHASES; BEHAVIOR; ALKANES; LIQUID}
}

@ARTICLE{KENW92,
  author = {P. R. Kenway and P. M. Oliver and S. C. Parker and D. C. Sayle and
	T. X. T. Sayle and J. O. Titiloye},
  title = {Computer Simulation of Surface Segregation},
  journal = MS,
  year = {1992},
  volume = {9},
  pages = {83--98},
  keywords = {surface segregation; impurities; energy minimization; Born model of
	solids; calcium; magnesium; zirconium}
}

@ARTICLE{Kerr92,
  author = {R.A. Kerr},
  title = {From Mercury to Pluto, chaos pervades the solar system},
  journal = SCI,
  year = {1992},
  volume = {257},
  pages = {33}
}

@ARTICLE{KITZ92,
  author = {E.~von Kitzing},
  title = {Modeling {DNA} Structure: Molecular Mechanics and Molecular Dynamics},
  journal = ME,
  year = {1992},
  volume = {211},
  pages = {449--467},
  annote = {general review of how to conduct MD or MM of DNA}
}

@ARTICLE{KJEL92,
  author = {M. Kjeldgaard and J. Nyborg},
  title = {Refined structure of elongation factor {EF-Tu} from {{\em Escherichia
	coli}}},
  journal = JMB,
  year = {1992},
  volume = {223},
  pages = {721--742}
}

@ARTICLE{KLEI92,
  author = {W. Kleinekofort and L. Germeroth and J. van der Broek and D. Schubert
	and H. Michel},
  title = {The light-harvesting complex {II} ({B}800/850) from {{\it{R}hodospirillum
	molischianum\/}} is an octamer},
  journal = {Biochimica et Biophysica Acta},
  year = {1992},
  volume = {1140},
  pages = {102--104}
}

@BOOK{KlPl92,
  title = {Numerical Solution of Stochastic Differential Equations},
  publisher = {Springer-Verlag},
  year = {1992},
  author = {Peter E. Kloeden and Eckhard Platen},
  volume = {23},
  series = {Applications of Mathematics: Stochastic Modelling and Applied Probability},
  address = {New York},
  note = {Second corrected printing 1995}
}

@ARTICLE{KOBA92,
  author = {T. Kobayashi and B. Storrie and K. Simons and C. G. Dotti},
  title = {A Functional Barrier to Movement of Lipids in Polarized Neurons},
  journal = NAT,
  year = {1992},
  volume = {359},
  pages = {647--650},
  number = {6396},
  address = {CG Dotti, European Molec Biol Lab, Cell Biol Program, Postfach 102209,
	W-6900 Heidelberg, Germany},
  annote = {requested Tx=19921105.},
  isbn = {0028-0836},
  keywords = {DEPENDENT SODIUM-CHANNELS; HIPPOCAMPAL-NEURONS; PLASMA-MEMBRANE; EPITHELIAL-CELL;
	INFLUENZA-VIRUS; TIGHT JUNCTIONS; GOLGI-APPARATUS; MAMMALIAN SPERM;
	MDCK CELLS; DOMAINS},
  publisher = {Macmillan Press Ltd, Brunel Rd, Houndmills, Basingstoke RG21 2XS,
	Hampshir, United Kingdom}
}

@ARTICLE{KoPe92,
  author = {J. Kolafa and J.~W. Perram},
  title = {Cutoff errors in the {E}wald summation formulae for point charge
	systems},
  journal = MS,
  year = {1992},
  volume = {9},
  pages = {351--368}
}

@BOOK{KORN92A,
  title = {{DNA} Replication},
  publisher = {W. H. Freeman and Company},
  year = {1992},
  author = {Arthur Kornberg and Tania A. Baker},
  address = {New York},
  edition = {2nd}
}

@INPROCEEDINGS{KORN92,
  author = {A. A. Kornyshev and S. Leikin},
  title = {Theory of Hydration Forces},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {83--86},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{KOTH92,
  author = {V.~Kothekar and A.~Kotwal},
  title = {Molecular mechanics simulation of the interaction of the estrogen
	receptor with estrogen regulatory element},
  journal = IJBB,
  year = {1992},
  volume = {29},
  pages = {322--329},
  annote = {31aa ER-DBD with 5bp of DNA, found {DNA}bend}
}

@ARTICLE{KRIS92,
  author = {S. M. Krisovitch and S. L. Regen},
  title = {Nearest-Neighbor Recognition in Phospholipid Membranes - a Molecular-level
	Approach to the Study of Membrane Suprastructure},
  journal = JACS,
  year = {1992},
  volume = {114},
  pages = {9828--9835},
  number = {25},
  address = {lehigh univ,dept chem, bethlehem, pa, 18015, lehigh univ,zettlemoyer
	ctr surface studies, bethlehem, pa, 18015, united states of america},
  annote = {A molecular-level approach has been devised for probing the lateral
	organization of phospholipid bilayers. This method is based on the
	equilibration of disulfide-based phospholipid dimers via thiolate-disulfide
	interchange reactions. Analysis of resulting product mixtures defines
	the tendency of one phospholipid monomer to become a covalently attached
	nearest neighbor of another. Investigation of equilibrium mixtures
	derived from dimeric analogs of 1,2-dimyristoyl-sn-glycero-3-phosphocholine
	(DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) has
	yielded conclusive evidence that the lipid monomers are randomly
	distributed throughout the membrane in the fluid phase and also in
	the gel-fluid coexistence region. Additional support for random organization
	in the gel-fluid region has been obtained by use of differential
	scanning calorimetry (DSC). When the difference in alkyl chain length
	between the equilibrating monomers is increased from two to four
	methylene groups (i.e., dimeric analogs of 1,2-distearoyl-sn-glycero-3-phosphocholine
	(DSPC) are used instead of DPPC), the membrane suprastructure remains
	random in the fluid phase. In the gel-fluid coexistence region, however,
	a significant deviation from randomness is observed. This deviation
	implies the presence of lipid domains and is consistent with the
	appearance of phase separation, as indicated by DSC analysis. Examination
	of the temperature dependence of this nearest-neighbor recognition
	supports the hypothesis that the packing forces that govern such
	recognition can be very similar to those that govern domain formation.
	Previous conclusions that have been drawn from quick-freeze DSC experiments
	with DMPC/DPPC bilayers are critically examined in light of these
	findings. requested Tx=19930108.},
  keywords = {differential-scanning-calorimetry. unilamellar-vesicles. phase. mixtures.
	volume. model}
}

@ARTICLE{KUBI92,
  author = {M.~G.~Kubinec and D.~E.~Wemmer.},
  title = {NMR evidence for DNA bound water in solution},
  journal = JACS,
  year = {1992},
  volume = {114},
  pages = {8739--8740}
}

@ARTICLE{KUMA92,
  author = {A.~Kumar and V.~Kothekar},
  title = {Stereochemical aspects of interactions of {DNA} binding domain of
	human progesterone receptor with d({AGGTCATGCT})$_2$},
  journal = {Indian Journal of Biochemistry and Biophysics},
  year = {1992},
  volume = {29},
  pages = {236--244},
  annote = {model building of hPR receptor complexed with {DNA} obtains many
	of the contacts that i obtain and mention distortion of the {DNA}from
	B form}
}

@ARTICLE{KBSK92,
  author = {Shankar Kumar and Djamal Bouzida and Robert H. Swendsen and Peter
	A. Kollman and John M. Rosenberg},
  title = {The weighted histogram analysis method for free-energy calculations
	on biomolecules. {I}: The method},
  journal = {J. Comput. Chem.},
  year = {1992},
  volume = {13},
  pages = {1011--1021},
  number = {8},
  address = {New York, NY, USA},
  doi = {http://dx.doi.org/10.1002/jcc.540130812},
  issn = {0192-8651},
  publisher = {John Wiley \& Sons, Inc.}
}

@ARTICLE{Kunt92,
  author = {Irwin D. Kuntz},
  title = {Structure-based strategies for drug design and discovery},
  journal = SCI,
  year = {1992},
  volume = {257},
  pages = {1078--1082}
}

@ARTICLE{KUSZ92,
  author = {Kuszewski, J. and Nilges, M. and A. T. Br{\"u}nger},
  title = {Sampling and Efficiency of Metric Matrix Distance Geometry: A Novel
	``Partial'' Metrization Algorithm},
  journal = {Journal of Biomolecular {NMR}},
  year = {1992},
  volume = {2},
  pages = {33--56}
}

@ARTICLE{KONI92,
  author = {Sabine K{\"o}nig and W. Pfeiffer and T. Bayerl and D. Richter and
	Erich Sackmann},
  title = {Molecular dynamics of lipid bilayers studied by incoherent quasi-elastic
	neutron scattering},
  journal = JPF,
  year = {1992},
  volume = {2},
  pages = {1589--1615},
  number = {8},
  annote = {time regime: 10^-13s...10^-9s; nice introduction; adds salt (NaCl)
	to increase hydration; packing desity plays major role for lipid
	dynamics; in LC phase of DPPC: CM long range diffusion D=0.0097*10^-5cm^2/s;
	transversal diffusion D=0.6*10^-5cm^2/s; lateral diffusion D=0.015...0.6
	*10^-5cm^2/s; also gives diffusion amplitudes; Sabine K\"onig workes
	with Sackmann in Munich: Sabine.Koenig@Physik.TU-Muenchen.DE},
  keywords = {membrane; DPPC; chain/headgroup dynamics; short range diffusive motions;
	gel phase; LC phase; kinks; diffusion; wobbling in a cone},
  suggestions = {study diffusion (mean displacement) depending on position in chain
	or headgroup (wobbling in a cone); investigate rotation of the lipids;
	look at correlation in the motions of lipids: is transversal diffusion
	correlated? If yes=>global ondulations of membrane; not only determine
	the long range diffusion constant, but also the short range one;
	are there any lipids exchanging places (hops)?}
}

@ARTICLE{LAAK92,
  author = {L. Laaksonen},
  title = {A graphics program for the analysis and display of molecular dynamics
	trajectories},
  journal = {Journal of Molecular Graphics},
  year = {1992},
  volume = {10},
  pages = {33--34}
}

@ARTICLE{LANY92,
  author = {J. K. Lanyi},
  title = {Proton-Transfer and Energy Coupling in the Bacteriorhodopsin Photocycle},
  journal = JBB,
  year = {1992},
  volume = {24},
  pages = {169--179}
}

@ARTICLE{LANY92A,
  author = {J. K. Lanyi and J. Tittor and G. V{\'a}r{\'o} and G. Krippahl and
	D. Oesterhelt},
  title = {Influence of the Size and Protonation State of Acidic Residue 85
	on the Absorption Spectrum and Photoreaction of the Bacteriorhodopsin
	Chromophore},
  journal = BBA,
  year = {1992},
  volume = {1099},
  pages = {102--110}
}

@ARTICLE{LASK92,
  author = {Laurence A. Lasky},
  title = {Selectins: Interpreters of Cell-Specific Carbohydrate Information
	During Inflammation},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {964--969}
}

@ARTICLE{LAUD92,
  author = {V.~Laudet and C.~H{\"a}nni and J.~Coll and F.~Catzeflis and D.~St{\'e}helin},
  title = {Evolution of the Nuclear Receptor Gene Superfamily},
  journal = EMBO,
  year = {1992},
  volume = {11},
  pages = {1003--1013},
  number = {3},
  annote = {very interesting history of nuclear receptors including classification,
	complete list of hormone receptors, related families}
}

@ARTICLE{LeWa92,
  author = {Frederick S. Lee and Arieh Warshel},
  title = {A Local Reaction Field Method for Fast Evaluation of Long-Range Electrostatic
	Interactions in Molecular Simulations},
  journal = {J. Chem.\ Phys.},
  year = {1992},
  volume = {97},
  pages = {3100--3107},
  number = {5}
}

@TECHREPORT{LeSk92b,
  author = {B. Leimkuhler and R.D. Skeel},
  title = {Symplectic numerical integrators in constrained {H}amiltonian systems},
  institution = {University of Kansas, Lawrence},
  year = {1992}
}

@INPROCEEDINGS{LEIS92,
  author = {C. E. Leiserson and Z. S. Abuhamdeh and D. C. Douglas and C. R. Feynman
	and M. N. Ganmukhi and J. V. Hill and W. D. Hillis and B. C. Kuszmaul
	and M. A. St. Pierre and D. S. Wells and M. C. Wong and S. W. Yang
	and R. Zak},
  title = {The Network Architecture of the {C}onnection {M}achine {CM--5}},
  booktitle = {Symposium on Parallel Algorithms and Architectures},
  year = {1992},
  annote = {The main technical document on the CM-5 is called the "CM-5 Technical
	Summary" available from Thinking Machines. More recently, this paper
	was published by Charles Leiserson et. al. on the CM-5 networks}
}

@ARTICLE{LEVI92,
  author = {Michael Levitt},
  title = {Accurate modeling of protein conformation by automatic segment matching},
  journal = JMB,
  year = {1992},
  volume = {226},
  pages = {507--533}
}

@BOOK{LEWI92,
  title = {Introduction to Parallel Computing},
  publisher = {Prentice Hall},
  year = {1992},
  author = {Lewis, T. G. and El-Rewini, H.},
  pages = {98--101},
  address = {Englewood Cliffs, New Jersey}
}

@ARTICLE{LILL92,
  author = {D. M. Lilley},
  title = {{HMG} has {DNA} wrapped up},
  journal = NAT,
  year = {1992},
  volume = {357},
  pages = {282--283}
}

@ARTICLE{LIN92,
  author = {Lin, S. L. and Mellor-Crummey, J. and Pettitt, B. M. and Phillips,
	Jr., G. N.},
  title = {The parallelization of {CHARMm} for the iPSC/860: molecular dynamics
	on a distributed computer},
  journal = {J. Comp. Chem.},
  year = {1992},
  note = {In press}
}

@ARTICLE{LOCK92,
  author = {David J.\ Lockhart and Peter S.\ Kim},
  title = {Internal Stark Effect Measurement of the Electric Field at the Amino
	Terminus of an $\alpha$ Helix},
  journal = SCI,
  year = {1992},
  volume = {257},
  pages = {947--951}
}

@ARTICLE{LOHM92,
  author = {T. M. Lohman and D. P. Mascotti},
  title = {Thermodynamics of Ligand-Nucleic Acid Interactions},
  journal = ME,
  year = {1992},
  volume = {212},
  pages = {400--424}
}

@ARTICLE{LOHM92a,
  author = {T. M. Lohman and D. P. Mascotti},
  title = {Nonspecific Ligand-{DNA} equilibrium binding parameters determined
	by fluorescence methods},
  journal = ME,
  year = {1992},
  volume = {212},
  pages = {424--458}
}

@PHDTHESIS{LORE92,
  author = {Michael Lorenz},
  title = {Strukturuntersuchungen am {Muskelprotein} {Aktin}: {R\"ontgen}faserdiffraktion
	und {Modellrechnungen}},
  school = {Ruprecht-Karls-Universit\"at Heidelberg, Germany},
  year = {1992}
}

@ARTICLE{LUNA92,
  author = {Elizabeth J. Luna and Anne L. Hitt},
  title = {Cytoskeleton---Plasma Membrane Interactions},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {955--964}
}

@ARTICLE{MACK92,
  author = {A. D. {MacKerell Jr.} and D. Bashford and M. Bellott and R. L. {Dunbrack
	Jr.} and J. Evanseck and M. J. Field and S. Fischer and J. Gao and
	H. Guo and S. Ha and D. Joseph and L. Kuchnir and K. Kuczera and
	F. T. K. Lau and C. Mattos and S. Michnick and T. Ngo and D. T. Nguyen
	and B. Prodhom and B. Roux and M. Schlenkrich and J. Smith and R.
	Stote and J. Straub and M. Watanabe and J. {Wiorkiewicz-Kuczera}
	and D. Yin and M. Karplus},
  title = {Self-consistent parameterization of biomolecules for molecular modeling
	and condensed phase simulations},
  journal = FASEB,
  year = {1992},
  volume = {A143},
  pages = {6},
  annote = {To cite CHARMM22 field for PROTEINS, cite this paper AND MACK98}
}

@ARTICLE{MAED92C,
  author = {A. Maeda and J. Sasaki and Y. J. Ohkita and M. Simpson and J. Herzfeld},
  title = {Tryptophan Perturbation in the {L} Intermediate of Bacteriorhodopsin:
	{Fourier} Transform Infrared Analysis with Indole-{$^{15}$N} Shift},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {12543--12545}
}

@ARTICLE{MAED92B,
  author = {A. Maeda and J. Sasaki and Y. Shishida and T. Yoshizawa},
  title = {Water Structural Changes in the Bacteriorhodopsin Photocycle: Analysis
	by {Fourier} Transform Infrared Spectroscopy},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {462--467}
}

@ARTICLE{MAED92A,
  author = {A. Maeda and J. Sasaki and Y. Shishida and T. Yoshizawa and M. Chang
	and B. Ni and R. Needleman and J. K. Lanyi},
  title = {Structures of Aspartic Acid-96 in the L and N Intermediates of Bacteriorhodopsin:
	Analysis by {Fourier} Transform Infrared Spectroscopy},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {4684--4690}
}

@ARTICLE{MAIE92,
  author = {E.J. Maier},
  title = {Spectral sensitivities including the ultraviolet of the passeriform
	bird {\em {L}eiothrix lutea}},
  journal = {J.~Comp.~Physiol.~A},
  year = {1992},
  volume = {170},
  pages = {709--714}
}

@ARTICLE{MaPa92,
  author = {E. Marinari and G. Parisi},
  title = {Simulated Tempering: A New {M}onte {C}arlo Scheme},
  journal = epl,
  year = {1992},
  volume = {19},
  pages = {451--458},
  abstract = {We propose a new global optimization method (Simulated Tempering)
	for simulating effectively a system with a rough free-energy landscape
	(i.e., many coexisting states) at finite nonzero temperature. This
	method is related to simulated annealing, but here the temperature
	becomes a dynamic variable, and the system is always kept at equilibrium.
	We analyse the method on the Random Field Ising Model, and we find
	a dramatic improvement over conventional Metropolis and cluster methods.
	We analyse and discuss the conditions under which the method has
	optimal performances.},
  annote = {simulated tempering reference, in Schu99}
}

@ARTICLE{MaKT92,
  author = {Glenn J. Martyna and Michael L. Klein and Mark E. Tuckerman},
  title = {{N}os\'e-{H}oover chains: The canonical ensemble via continuous dynamics},
  journal = {J. Chem. Phys.},
  year = {1992},
  volume = {97},
  pages = {2635--2643},
  number = {4}
}

@ARTICLE{MATT92,
  author = {Kathleen S. Matthews},
  title = {{DNA} looping},
  journal = {Microbiological Reviews},
  year = {1992},
  volume = {56},
  pages = {123--136},
  number = {1}
}

@ARTICLE{MCKI92,
  author = {S. J. McKinnon and S. L. Whittenburg and B. Brooks},
  title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion
	Through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {10497--10506},
  number = {25},
  abstract = {The effect of varying concentrations of cholesterol on the static
	properties of a hexadecane monolayer and on the diffusion rate of
	oxygen across the monolayer has been studied by using a novel application
	of nonequilibrium molecular dynamics. The results show an increased
	ordering of the hexadecane chains in the region of the monolayer
	near the added cholesterol with a general increase in monolayer thickness
	with increasing concentration of cholesterol. The calculation of
	the diffusion coefficients from the work required to pull oxygen
	through the monolayer by using a forcing potential suggests an enhanced
	diffusion rate of oxygen with added cholesterol and a decrease in
	the diffusion coefficient at higher cholesterol concentrations.},
  address = {LOUISIANA STATE UNIV,CTR EYE, BATON ROUGE, LA, 70803. UNIV NEW ORLEANS,DEPT
	CHEM, NEW ORLEANS, LA, 70148. NIH, BETHESDA, MD, 20892.},
  annote = {requested Tx=19930123.},
  keywords = {nuclear-magnetic-resonance. lipid-protein-interactions. proton-transfer-reactions.
	sodium-octanoate-micelle. consistent-force-field. {M}onte {C}arlo.
	computer-simulation. liquid-crystals. spin-label. bilayer-membranes.}
}

@ARTICLE{McAt92,
  author = {R. I. McLachlan and P. Atela},
  title = {The Accuracy of Symplectic Integrators},
  journal = {Nonlinearity},
  year = {1992},
  volume = {5},
  pages = {541--562}
}

@ARTICLE{MECK92,
  author = {R.U. Meckenstock and K. Krusche and R.A. Brunisholz and H. Zuber},
  title = {The Light-harvesting core-complex and the {B}820-subunit from {{\em
	{R}hodopseudomonas marina}}. {P}art {II}. Electron microscopic characterisation},
  journal = {FEBS Letters},
  year = {1992},
  volume = {311},
  pages = {135--138}
}

@ARTICLE{MeHF92,
  author = {B. Mehlig and D. W. Heermann and B. M. Forrest},
  title = {Hybrid {M}onte {C}arlo Method for Condensed-Matter Systems},
  journal = {Phys.\ Rev.\ B},
  year = {1992},
  volume = {45},
  pages = {679--685},
  number = {2},
  nremark = {In connection with symplecticness there is further evidence in support
	in that it is enough to have volume-preserving, reversible integrators
	for hybrid MC.}
}

@ARTICLE{METZ92,
  author = {G. Metz and F. Siebert and M. Engelhard},
  title = {Asp-85 is the Only Internal Aspartic Acid That Gets Protonated in
	the {M} Intermediate and the Purple-to-Blue Transition of Bacteriorhodopsin},
  journal = FEBS,
  year = {1992},
  volume = {303},
  pages = {237}
}

@BOOK{MeHa92,
  title = {Introduction to {H}amiltonian Dynamical Systems and the $N$-body
	Problem},
  publisher = {Springer-Verlag},
  year = {1992},
  author = {K.R. Meyer and G.R. Hall},
  nremark = {review on page 659 of SIREV 93}
}

@ARTICLE{MIMU92,
  author = {M. Mimuro and U. Nagashima and S. Takaichi and Y. Nishimura and I.
	Yamazaki and T. Katoh},
  title = {Molecular structure and optical properties of carotenoids for the
	in vivo energy transfer function in the algal photosynthetic pigment
	system},
  journal = BBA,
  year = {1992},
  volume = {1098},
  pages = {271--274}
}

@ARTICLE{MINI92,
  author = {A. Minnich and X. Collet and A. Roghani and C. Cladaras and R. L.
	Hamilton and C. J. Fielding and V. I. Zannis},
  title = {Site-Directed Mutagenesis and Structure-Function Analysis of the
	Human Apolipoprotein {A-I}},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {16553--16560}
}

@ARTICLE{MiKo92,
  author = {Shuichi Miyamoto and Peter A. Kollman},
  title = {{SETTLE}: An Analytical Version of the {SHAKE} and {RATTLE} Algorithm
	for Rigid Water Molecules},
  journal = JCC,
  year = {1992},
  volume = {13},
  pages = {952--962},
  number = {8}
}

@ARTICLE{MIYA92,
  author = {Tsutomu Miyasaka and Koichi Koyama and Isamu Itoh},
  title = {Quantum Conversion and Image Detection by a Bacteriorhodopsin-Based
	Artificial Photoreceptor},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {342--344},
  annote = {they built a pixel sensor (8 x 8) out of bR sensory elements}
}

@ARTICLE{MOE92,
  author = {J.~G.~Moe and I.~M.~Russu.},
  title = {Kinetics and energetics of base-pair opening in 5'-d{(CGCGAATTCGCG)}-3'
	and a substituted dodecamer containing {GT} mismatches},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {8421--8428}
}

@BOOK{Mohr92,
  title = {Finite Elements for Solids, Fluids, and Optimization},
  publisher = {Oxford Univ.\ Press},
  year = {1992},
  author = {G. A. Mohr},
  address = {New York}
}

@BOOK{MOOR92,
  title = {Electromagnetic Fields and Circadian Rhythmicity},
  publisher = {Birkh\"auser},
  year = {1992},
  author = {M.C. Moore-Ede and S.S. Campbell and R.J. Reiter},
  address = {Boston}
}

@ARTICLE{MOSS92,
  author = {R. A. Moss and S. Bhattacharya},
  title = {Kinetic Evidence for Interdigitation in Model Lipid Bilayers},
  journal = JPOC,
  year = {1992},
  volume = {5},
  pages = {467--470},
  number = {8},
  annote = {requested Tx=19921007.; flip-flop is movement of one lipid from one
	layer of the bilayer to the other layer},
  keywords = {ion vesicles; fatty acids; flip-flop; membranes; dynamics}
}

@ARTICLE{MOUR92,
  author = {O.G. Mouritsen and K. J{\"o}rgensen},
  title = {Dynamic lipid-bilayer heterogeneity: a mesoscopic vehicle for membrane
	function?},
  journal = {BioEssays},
  year = {1992},
  volume = {14},
  pages = {129--136}
}

@ARTICLE{MULL92A,
  author = {Urs A. Muller and Bernhard Baumle and Anton Gunzinger and Walter
	Guggenbuhl},
  title = {Achieving Supercomputer Performance for Neural Net Simulation with
	an Array of Digital Signal Processors},
  journal = IEEEM,
  year = {1992},
  pages = {55--64},
  annote = {same computer as in van Gunsterens work; uses Motorola 96002 DSP;
	quite impressive performance figures; one 96002 is about 8.8 times
	as fast as a T800 Transputer}
}

@ARTICLE{NARD92,
  author = {A.~M.~Nardulli and D.~J.~Shapiro},
  title = {Binding of the Estrogen Receptor {DNA}-Binding Domain to the Estrogen
	Response Element Induces {DNA} Bending},
  journal = {Molecular and Cellular Biology},
  year = {1992},
  volume = {12},
  pages = {2037--2042},
  annote = {SABB92 should also be cited as the other bending paper}
}

@ARTICLE{NELS92,
  author = {W. James Nelson},
  title = {Regulation of Cell Surface Polarity from Bacteria to Mammals},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {948--955}
}

@ARTICLE{NER92,
  author = {S. S. Ner},
  title = {{DNA}-binding proteins {HMGs} Everywhere},
  journal = {Current Biology},
  year = {1992},
  volume = {2},
  pages = {208--210},
  number = {4}
}

@ARTICLE{NIED92,
  author = {Christoph Niedermeier and Klaus Schulten},
  title = {Molecular Dynamics Simulations in Heterogenous Dielectrica and {D}ebye-{H}\"uckel
	Media: {A}pplication to the Protein Bovine Pancreatic Trypsin Inhibitor},
  journal = MS,
  year = {1992},
  volume = {8},
  pages = {361--387},
  number = {6},
  keywords = {BPTI}
}

@ARTICLE{NIKA92,
  author = {Horoshi Nikaido and Milton H. Saier, Jr.},
  title = {Transport Proteins in Bacteria: Common Themes in Their Design},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {917--924}
}

@ARTICLE{NIKO92,
  author = {E.~P.~Nikonowicz and D.~G.~Gorenstein},
  title = {Comparison of the X-ray Crystal, {NMR} Solution, and Molecular Dynamics
	Calculated Structures of a Tandem G$.$A Mismatched Oligonucleotide
	Duplex},
  journal = JACS,
  year = {1992},
  volume = {114},
  pages = {7494--7503},
  annote = {MD with water and counterions and also in vacum, amber, ions 3.0
	\AA from p in p-o-p bisector, shake all atoms?, 7\AA solvation shell,
	constant pressure and constant temp, 2fs timestep, DOES NOT SEEM
	VERY GOOD MD, but also contains much other NMR and Xstal data}
}

@ARTICLE{NYBE92,
  author = {A. Nyberg and T. Schlick},
  title = {On Increasing the Time Step in Molecular Dynamics},
  journal = CPL,
  year = {1992},
  volume = {198},
  pages = {538}
}

@ARTICLE{OBCE92,
  author = {Ceferino H. Obcemea and Branislav Vidic},
  title = {Bilipid layer molecular organization in P$_\beta$ phase studied by
	scanning tunneling microscopy},
  journal = UM,
  year = {1992},
  volume = {42},
  pages = {1019--1024},
  number = {B},
  address = {CH Obcemea, Georgetown Univ, Med Ctr, Dept Radiat Med, 3800 Reservoir
	Rd NW, Washington, DC 20007},
  annote = {detected asymmetry in riples; average surface roughness of 21\pm4\AA},
  isbn = {0304-3991},
  keywords = {DMPC; ripple phase; experimental},
  publisher = {Elsevier Science Publishers BV, PO Box 211, 1000 AE Amsterdam, Netherlands}
}

@ARTICLE{OBER92C,
  author = {Klaus Obermayer and Gary G. Blasdel and Klaus Schulten},
  title = {Statistical-Mechanical Analysis of Self-Organization and Pattern
	Formation During the Development of Visual Maps},
  journal = PRA,
  year = {1992},
  volume = {45},
  pages = {7568--7589},
  number = {10},
  annote = {May 15, 1992. Early version had a different title: ``Statistical-Mechanical
	... formation in the primary visual cortex of the macaque.''},
  tbtechrep = {TB-92-03}
}

@ARTICLE{OBY-92C,
  author = {Klaus Obermayer and Gary G. Blasdel and Klaus Schulten},
  title = {Statistical-Mechanical Analysis of Self-Organization and Pattern
	Formation During the Development of Visual Maps},
  journal = PRA,
  year = {1992},
  volume = {45},
  pages = {7568--7589},
  number = {10},
  annote = {May 15, 1992. Early version had a different title: ``Statistical-Mechanical
	... formation in the primary visual cortex of the macaque.''},
  tbtechrep = {TB-92-03}
}

@ARTICLE{OBER91,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {A Model for the Development of the Spatial Structure of Retinotopic
	Maps and Orientation Columns},
  journal = IEICECCS,
  year = {1992},
  volume = {{E75-A}},
  pages = {537--545},
  number = {5},
  note = {Reprinted in {\em The Principles of Organization in Organisms ---
	{S}anta {F}e {I}nstitute Studies in the Sciences of Complexity, Vol.~{XII}.}
	A.\ Baskin and J.\ Mittenthal, Eds. (Addison Wesley, 1991)},
  annote = {In the book version, the pages are 141--166.}
}

@INCOLLECTION{ObSB92,
  author = {Klaus Obermayer and Klaus Schulten and Gary G. Blasdel},
  title = {A Comparison Between a Neural Network Model for the Formation of
	Brain Maps and Experimental Data},
  booktitle = {Advances in Neural Information Processing Systems~4},
  publisher = {Morgan Kaufmann Publishers},
  year = {1992},
  editor = {D. S. Touretzky and R. Lippman},
  pages = {83--90},
  tbtechrep = {TB-91-01}
}

@ARTICLE{OEST92,
  author = {D. Oesterhelt and J. Tittor and E. Bamberg},
  title = {A Unifying Concept for Ion Translocation in Retinal Proteins},
  journal = JBB,
  year = {1992},
  volume = {24},
  pages = {181--191}
}

@TECHREPORT{Okun92a,
  author = {D.~Okunbor},
  title = {Canonical Numerical Integrators for {H}amiltonian Dynamical Systems},
  institution = {Dept. of Computer Sci., Univ. of Illinois at Urbana-Champaign, Urbana,
	Illinois, USA},
  year = {1992},
  number = {UIUCDCS-R-92-1785},
  note = {(Ph.D. Thesis)}
}

@ARTICLE{Okun92b,
  author = {D. Okunbor},
  title = {Canonical Methods for {H}amiltonian Systems: Numerical Experiments},
  journal = {Physica D},
  year = {1992},
  volume = {60},
  pages = {314--322}
}

@ARTICLE{OkSk92a,
  author = {D. Okunbor and R.~D. Skeel},
  title = {An explicit Runge-Kutta-Nystrom method is canonical if and only if
	its adjoint is explicit},
  journal = SJNA,
  year = {1992},
  volume = {29},
  pages = {521--527}
}

@ARTICLE{OkSk92b,
  author = {D. Okunbor and R.~D. Skeel},
  title = {Explicit canonical methods for {H}amiltonian systems},
  journal = {Math. Comput.},
  year = {1992},
  volume = {59},
  pages = {439--455},
  number = {200}
}

@ARTICLE{OLEJ92,
  author = {J. Olejnik and B. Brzezinski and G. Zundel},
  title = {A Proton Pathway with Large Proton Polarizability and the Proton
	Pumping Mechanism in Bacteriorhodopsin --- {Fourier} Transform Difference
	Spectra of Photoproducts of Bacteriorhodopsin and of Its Pentademethyl
	Analogue},
  journal = JMS,
  year = {1992},
  volume = {271},
  pages = {157--173},
  number = {3},
  annote = {requested Tx=19921007.},
  keywords = {retinal {Schiff}-base; intermolecular Hydrogen bonds; vibrational
	spectroscopy; neutron diffraction; purple membrane; infrared spectroscopy;
	intramolecular chain; transfer equilibrium; biological systems; structural
	changes}
}

@ARTICLE{ORLO92,
  author = {A. Orlova and E. H. Egelman},
  title = {Structural Basis for the Destabilization of {F}-Actin by Phosphate
	release following {ATP} hydrolysis},
  journal = JMB,
  year = {1992},
  volume = {227},
  pages = {1043--1053}
}

@BOOK{OsKe92,
  title = {Troff User's Manual},
  publisher = {Bell Laboratories},
  year = {1992},
  author = {Ossanna, J. and Kernighan, B. F.},
  address = {Murray Hill}
}

@ARTICLE{PABO92,
  author = {C. O. Pabo and R. T. Sauer},
  title = {Transcription factors: structural families and principles of {DNA}
	recognition},
  journal = ARB,
  year = {1992},
  volume = {61},
  pages = {1053--1095}
}

@ARTICLE{PEAR92,
  author = {R. M. Pearlstein},
  title = {Theory of the optical spectra of the bacteriochlorophyll a antenna
	prote in trimer from {{\em Prosthecochloris aestuarii}}},
  journal = {Photosynthesis Research},
  year = {1992},
  volume = {31},
  pages = {213--226}
}

@ARTICLE{PeWa92,
  author = {Jeffrey W. Peng and Gerhard Wagner},
  title = {Mapping of the Spectral Densities of {N}-{H} Bond Motions in Eglin
	{C} Using Heteronuclear Relaxation Experiments},
  journal = {Biochemistry},
  year = {1992},
  volume = {31},
  pages = {8571--8586}
}

@ARTICLE{PERK92,
  author = {G. A. Perkins and E. Liu and F. Burkard and E. A. Berry and R. M.
	Glaeser},
  title = {Characterization of the Conformational Change in the {M$_1$} and
	{M$_2$} Substates of Bacteriorhodopsin by the Combined Use of Visible
	and Infrared Spectroscopy},
  journal = JSB,
  year = {1992},
  volume = {109},
  pages = {142--151}
}

@ARTICLE{PETE92b,
  author = {A.R. Peters and N. Dekker and L. van den Berg and R. Boelens and
	R. Kaptein and A. J. Slotboom and G. H. de Haas},
  title = {Conformational Changes in phospholipase {A$_2$} upon binding to micellar
	interfaces in the absence and presence of competetive inhibitors.
	{ A }$^1${H} and $^{15}${NMR} study},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {10024--10030}
}

@ARTICLE{PETE92A,
  author = {I. R. Peterson},
  title = {Phases of Amphiphilic Monolayers in Different Environments},
  journal = PHYS,
  year = {1992},
  volume = {32},
  pages = {245--247},
  number = {46},
  address = {UNIV MAINZ,INST PHYS CHEM,JAKOB WELDER WEG 11, W-6500 MAINZ, GERMANY},
  annote = {Amphiphiles are organic molecules which spontaneously form two-dimensional
	phases, particularly at pre-existing interfaces. This is the physical
	basis for cell membranes and detergents, and is very important in
	colloidal systems. Recently available techniques have provided proof
	that monolayers of many amphiphiles display a rich variety of phases.
	Many of these phases display behaviour characteristic for low-dimensional
	(i.e. highly anisotropic) systems, and some are hexatic. In addition
	to the experimental conditions of surface pressure and temperature,
	the particular phase adopted by a monolayer depends on the chain
	length, the headgroup and its environment. The present paper shows
	that, although not all structures are possible, the same structures
	recur under suitable conditions with different headgroups and different
	environments, including the commensurate environment provided by
	a multilayer structure. The common factor limiting the choice of
	structure appears to be the aliphatic chains, and the particular
	structure which actually occurs appears to be determined by interaction
	of the environment with the headgroups. This idea is developed and
	shown to predict correctly the variation with chain length of two
	of the upright-to-tilted phase transitions observed in monolayers
	on the water surface. It is possible to talk about a bulk pressure
	within the monolayer, which is influenced by the interactions at
	the monolayer interfaces and which controls the molecular tilt.},
  keywords = {CHAIN-FATTY-ACIDS; ORIENTATIONAL-ORDER; amphiphiles; membrane; crystallography}
}

@ARTICLE{PETE92,
  author = {Mark A. Peterson and Helmut Strey and Erich Sackmann},
  title = {Theoretical and phase contrast microscopic eigenmode analysis of
	erythrocyte flicker: amplitudes},
  journal = JPF,
  year = {1992},
  volume = {2},
  pages = {1273--1285},
  annote = {shows pictures which remind me of Dan and Benno: diffusional edge
	enhancement; not relevant for study of biological membranes}
}

@ARTICLE{PHIL92,
  author = {J.B. Philipps and S.C. Borland},
  title = {Magnetic compass orientation is eliminated under near-infrared light
	in the eastern red-spotted newt {\em {N}otophtalmus viridescens}},
  journal = {Anim.~Behav.},
  year = {1992},
  volume = {44},
  pages = {796--797}
}

@ARTICLE{PHIL92A,
  author = {J.B. Philipps and S.C. Borland},
  title = {Behavioral evidence for use of a light-dependent magnetoreception
	mechanism by a vertebrate},
  journal = NAT,
  year = {1992},
  volume = {359},
  pages = {142--144}
}

@ARTICLE{PIL92,
  author = {P. M. Pil and S. J. Lippard},
  title = {Specific binding of chromosomal protein {HMG1} to {DNA} damaged by
	the anticancer drug cisplatin},
  journal = SCI,
  year = {1992},
  volume = {256},
  pages = {234--237}
}

@ARTICLE{POLL92A,
  author = {Thomas D. Pollard and Ilya Goldberg and William H. Schwarz},
  title = {Nucleotide Exchange, Structure, and Mechanical Properties of Filaments
	Assembled from {ATP}-actin and {ADP}-actin},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {20339--20345}
}

@ARTICLE{POLL92,
  author = {W. T. Pollard and S. L. Dexheimer and Q. Wang and L. A. Peteanu and
	C. V. Shank and R. A. Mathies},
  title = {Theory of Dynamics Absorption Spectroscopy of Nonstationary States.
	4. {A}pplication to {12-fs} Resonant Impulsive Raman Spectroscopy
	of Bacteriorhodopsin},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {6147--6158}
}

@INPROCEEDINGS{POWN92,
  author = {H. J. Pownall and Gotto, Jr., A. M.},
  title = {Human plasma apolipoproteins},
  booktitle = {Biology and Medicine in Structure and Function of Apolipoproteins},
  year = {1992},
  editor = {M. Rosseneu},
  pages = {1--32},
  address = {Boca Raton, FL},
  publisher = {CRC Press}
}

@BOOK{PRES92,
  title = {Numerical Recipes in C},
  publisher = {Cambridge University Press},
  year = {1992},
  author = {William H. Press and Saul A. Teukolsky and William T. Vetterling
	and Brian P. Flannery},
  address = {New York},
  edition = {2}
}

@BOOK{PTAS92,
  title = {A Genetic Switch},
  publisher = {Cell Press \& Blackwell Scientific Publications},
  year = {1992},
  author = {Mark Ptashne},
  address = {Cambridge, MA},
  edition = {2nd}
}

@ARTICLE{PUET92,
  author = {Benno P{\"u}tz and Daniel Barsky and Klaus Schulten},
  title = {Edge Enhancement by Diffusion in Microscopic Magnetic Resonance Imaging},
  journal = JMR,
  year = {1992},
  volume = {97},
  pages = {27--53},
  tbtechrep = {TB-91-01}
}

@ARTICLE{QiZh92,
  author = {M.-Z. Qin and M.-Q. Zhang},
  title = {Symplectic {R}unge-{K}utta schemes for {H}amiltonian system},
  journal = {J.\ Comput.\ Math.},
  year = {1992},
  volume = {Supplementary Issue},
  pages = {205--215}
}

@ARTICLE{ALOI92,
  author = {R.C.Aloia and C.C.Curtrain and F.C.Jensen},
  title = {Mebrane Cholesteral and Human Immunodeficiency Virus Infectivity},
  journal = {FIXME},
  year = {1992},
  pages = {283--303},
  booktitle = {Membrane Interactions of HIV},
  publisher = {Wiley-Liss, Inc.}
}

@ARTICLE{RADM92,
  author = {M. Radmacher and R. W. Tillmann and M. Fritz and Hermann E. Gaub},
  title = {From Molecules to Cells: Imaging Soft Samples with the Atomic Force
	Microscope},
  journal = SCI,
  year = {1992},
  volume = {257},
  pages = {1900--1905},
  annote = {article suggested by KS/Sackmann/Gaub: hot stuff},
  keywords = {membrane; experimental; AFM},
  suggestions = {produce pictures similar to theirs: use Gauss volumes}
}

@INPROCEEDINGS{RADM92B,
  author = {M. Radmacher and R. M. Zimmermann and Hermann E. Gaub},
  title = {Does the Scanning Force Microscope Resolve Individual Lipid Molecules?},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {24--29},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{RAGH92,
  author = {K.\ Raghavan and M.\ Rami Reddy and Max L.\ Berkowitz},
  title = {A Molecular Dynamics Study of the Structure and Dynamics of Water
	between Dilauroylphosphatidylethanolamine Bilayers},
  journal = LM,
  year = {1992},
  volume = {8},
  pages = {233--240},
  number = {1},
  annote = {with ab initio charges for DLPE; investigates head group structure,
	atom-atom correlation functions, atom density profiles across headgroup
	and water regions, hydrogen bond profiles, water diffusion and polarization}
}

@ARTICLE{RAGA92,
  author = {I. Ragos and M. Robb and F. Bernardi and M. Ollivuci},
  title = {Optimization and Characterization of the Lowest Energy Point on a
	Conical Intersection using an {MC-SCF} Lagrangian.},
  journal = CPL,
  year = {1992},
  volume = {197},
  pages = {217}
}

@ARTICLE{RAI92,
  author = {S. Rai and R. Buenker},
  title = {A Theoretical Investigation of the Lowest Bu State of {\it trans}-Butadiene.},
  journal = {Indian Journal of Chemistry},
  year = {1992},
  volume = {31},
  pages = {215--218}
}

@ARTICLE{RAPO92,
  author = {Tom A. Rapoport},
  title = {Transport of Proteins Across the Endoplasmic Reticulum Membrane},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {931--936}
}

@ARTICLE{REDD92,
  author = {N.R.S. Reddy and R. Picorel and G.J. Small},
  title = {B896 and B870 Components of the {R}hodobacter-sphaeroides Antenna
	- a Hole Burning Study},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {6458--6464}
}

@ARTICLE{REHB92,
  author = {P.~Rehberger and M.~Rexin and U.~Gehring},
  title = {Heterotetrameric structure of the human progesterone receptor},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {8001--8005}
}

@ARTICLE{RENT91,
  author = {R. Renthal and R. Regalado},
  title = {Cooperativity of the Dehydration Blue-Shift of Bacteriorhodopsin},
  journal = PCPB,
  year = {1992},
  volume = {54},
  pages = {931--935}
}

@ARTICLE{REXI92,
  author = {M.~Rexin and W.~Busch and B.~Segnitz and U.~Gehring},
  title = {Structure of the glucocorticoid receptor in intact cells in the absence
	of hormone},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {9619--9621}
}

@ARTICLE{REYN92,
  author = {L. J. Reynolds and L. L. Hughes and E. A. Dennis},
  title = {Analysis of Human Synovial Fluid Phospholipase {A}$_2$ on short chain
	Phosphatidylcholine-Mixed Micelles: Development of a Spectrophotometric
	Assay Suitable for a Microtiterplate Reader},
  journal = {Analytical Biochemistry},
  year = {1992},
  volume = {204},
  pages = {190--197}
}

@ARTICLE{RING92,
  author = {A. Ring},
  title = {influence of ion occupancy and membrane deformation of gramicidin
	A channel stability in lipid membranes},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {1306--1365}
}

@BOOK{RITT92,
  title = {Textbook: Neural Computation and Self-Organizing Maps: An Introduction},
  publisher = {Ad\-di\-son-Wesley},
  year = {1992},
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  address = {New York},
  edition = {Revised {E}nglish}
}

@ARTICLE{ROHR92,
  author = {M. Rohr and W. Gartner and G. Schweitzer and A. R. Holzwarth and
	S. E. Braslavsky},
  title = {Quantum Yields of the Photochromic Equilibrium Between Bacteriorhodopsin
	and Its Bathointermediate-K - Femtosecond and Nanosecond Optoacoustic
	Spectroscopy},
  journal = JPC,
  year = {1992},
  volume = {96},
  pages = {6055--6061},
  number = {14},
  address = {W Gartner, Max Planck Inst Strahlenchem, Stifstr 34-36, W-4330 Mulheim,
	Germany},
  annote = {requested Tx=19920901., at binding},
  keywords = {RESONANCE RAMAN-SPECTROSCOPY; RETINAL CHROMOPHORE; PROTONATION CHANGES;
	PURPLE MEMBRANE; PHOTOCYCLE; PICOSECOND; EFFICIENCY; CONFIGURATION;
	PHOTOPRODUCT; SCATTERING}
}

@BOOK{Ross92,
  title = {Morphogenesis},
  publisher = {Marcel-Dekker},
  year = {1992},
  author = {E. F. Rossomando},
  address = {New York}
}

@ARTICLE{ROTH92A,
  author = {K. J. Rothschild and Y. W. He and S. Sonar and T. Marti and H. G.
	Khorana},
  title = {Vibrational Spectroscopy of Bacteriorhodopsin Mutants - Evidence
	That {Thr}-46 and {Thr}-89 Form Part of a Transient Network of Hydrogen
	Bonds},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {1615--1622}
}

@ARTICLE{RADL92,
  author = {Joachim R{\"a}dler and Erich Sackmann},
  title = {On the Measurement of Weak Repulsive and Frictional Colloidal Forces
	by Reflection Interference Contrast Microscopy},
  journal = LM,
  year = {1992},
  volume = {8},
  pages = {848--853},
  annote = {not relevant for study of biological membranes; may be it is after
	all, as a technique!},
  keywords = {friction; DMPC}
}

@INPROCEEDINGS{RADL92A,
  author = {Joachim R{\"a}dler and Erich Sackmann},
  title = {Vesicle--Substrate Interaction Studied by Reflection Interference
	Contrast Microscopy},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {158--161},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{SABB92,
  author = {M.~Sabbah and S.~Le Ricousse and G.~Redeuith and E.~Baulieu},
  title = {Estrogen Receptor--Induced Bending of the {{\em Xenopus Vitellogen}}
	in {A}$_2$ Gene Hormone Response Element},
  journal = {Biochem.\ and Biophys.\ Res.\ Comm.},
  year = {1992},
  volume = {185},
  pages = {944--952},
  number = {3},
  annote = {cite this as the other bending paper when citing NARD92}
}

@ARTICLE{Sanz92a,
  author = {J. M. Sanz-Serna},
  title = {Symplectic Integrators for {H}amiltonian Problem: an Overview},
  journal = {Acta Numerica},
  year = {1992},
  volume = {1},
  pages = {243--286},
  nremark = {CSX 519.4AC82}
}

@INPROCEEDINGS{Sanz92c,
  author = {J. M. Sanz-Serna},
  title = {The Numerical Integration of {H}amiltonian Systems},
  booktitle = {Computational Ordinary Differential Equations},
  year = {1992},
  editor = {J. R. Cash and I. Gladwell},
  organization = {Oxford Univ. Press},
  nremark = {Proc. of IMA Conference on Computational Differential Equations, Imperial
	College, London, July, 1989}
}

@ARTICLE{SASA92,
  author = {H. Sasabe and T. Furuno and J. Otomo and H. Tomioka and Y. Urabe
	and T. Nagamune and K. H. Kim and K. Kobayashi and Y. Kobayashi},
  title = {2-Dimensional Molecular Packing of Proteins},
  journal = TSF,
  year = {1992},
  volume = {216},
  pages = {99--104},
  number = {1},
  address = {H Sasabe, Inst Phys \& Chem Res, Frontier Res Program, 2-1 Hirosawa,
	Wako, Saitama 35101, Japan},
  annote = {requested Tx=19920925.},
  keywords = {BACTERIORHODOPSIN; MEMBRANE},
  publisher = {Elsevier Sequoia SA, PO Box 564, 1001 Lausanne 1, Switzerland}
}

@ARTICLE{SASA92A,
  author = {J. Sasaki and Y. Shichida and J. K. Lanyi and A. Maeda},
  title = {Protein Changes Associated with Reprotonation of the Schiff Base
	in the Photocycle of {ASP(96) $\rightarrow$ ASN} Bacteriorhodopsin
	-- The {M(N)} Intermediate with Unprotonated Schiff Base But {N}-like
	Protein Structure},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {20782--20786}
}

@ARTICLE{SATO92,
  author = {C. Sato and G. Matsumoto},
  title = {Proposed tertiary structure of the sodium channel},
  journal = BBRC,
  year = {1992},
  volume = {186},
  pages = {1158--1167}
}

@ARTICLE{SCHA92,
  author = {B. Scharf and B. Hess and M. Engelhard},
  title = {Chromophore of Sensory Rhodopsin II from {{\em Halobacterium halobium}}},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {12486--12492}
}

@ARTICLE{SCHL92A,
  author = {Robert Schleif},
  title = {{DNA} looping},
  journal = ARB,
  year = {1992},
  volume = {61},
  pages = {199--223}
}

@ARTICLE{ScFo92a,
  author = {T. Schlick and A. Fogelson},
  title = {{TNPACK}---a Truncated {N}ewton Minimization Package for Large-Scale
	Problems: {I}. {A}lgorithm and Usage},
  year = {1992},
  volume = {18},
  pages = {46--70},
  number = {46}
}

@ARTICLE{ScFo92b,
  author = {T. Schlick and A. Fogelson},
  title = {{TNPACK}---a Truncated {N}ewton Minimization Package for Large-Scale
	Problems: {II}. {A}pplications},
  journal = ACMTMS,
  year = {1992},
  volume = {18},
  pages = {71--111},
  number = {46}
}

@ARTICLE{OLSO92,
  author = {T. Schlick and W. Olson},
  title = {Supercoiled {DNA} energetics and dynamics by computer simulation},
  journal = JMB,
  year = {1992},
  volume = {223},
  pages = {1089--1119}
}

@ARTICLE{ScOl92,
  author = {T. Schlick and W. K. Olson},
  title = {Supercoiled {DNA} Energetics and Dynamics by Computer Simulation},
  journal = {J. Mol.\ Biol.},
  year = {1992},
  volume = {223},
  pages = {1089--1119}
}

@ARTICLE{SCHN92A,
  author = {B.~Schneider and D.~Cohen and H.~M.~Berman},
  title = {Hydration of {DNA} bases: analysis of crystallographic data},
  journal = {Biopolymers},
  year = {1992},
  volume = {32},
  pages = {725--750}
}

@ARTICLE{ScSt92,
  author = {H. Schreiber and O. Steinhauser},
  title = {Taming Cut-off Induced Artifacts in Molecular Dynamics Studies of
	Solvated Polypeptides},
  journal = {J. Mol.\ Biol.},
  year = {1992},
  volume = {228},
  pages = {909--923}
}

@INPROCEEDINGS{SCHU92,
  author = {Klaus Schulten},
  title = {Computational Biology on Massively Parallel Machines},
  booktitle = {Parallel Computation~--- {P}roceedings of the First International
	{ACPC} Conference, Salzburg, Austria},
  year = {1992},
  pages = {391--400},
  address = {New York},
  publisher = {Springer}
}

@INBOOK{SCHU92A,
  title = {Fluorescence studies of nucleic acids: dynamics, rigidities, and
	structures},
  publisher = {Plenum Press},
  year = {1992},
  author = {J. Michael Schurr and B. S. Fujimoto and P. Wu and L. Song},
  volume = {3},
  series = {Topics in fluorescence spectroscopy},
  address = {New York},
  booktitle = {Biochemical apllications}
}

@ARTICLE{SCOT92,
  author = {W. Scott and A. Gunzinger and B. B{\"a}umle and P. Kohler and U.
	A. M{\"u}ller and H-R. Vonder M{\"u}hll and A. Eichenberger and W.
	Guggenb{\"u}hl and N. Ironmonger and F. M{\"u}ller-Plathe and W.
	F. van Gunsteren},
  title = {Parallel Molecular Dynamics on a Multi Signalprocessor System},
  journal = CPC,
  year = {1992},
  note = {submitted},
  annote = {only vdW fluids, planned for real MD with long range Coulomb IA later
	on, DSP: Motorola 96002 in assembler},
  keywords = {parallel processing; molecular dynamics}
}

@ARTICLE{SEGR92,
  author = {J. P. Segrest and M. K. Jones and H. DeLoof and C. G. Brouillette
	and Y. V. Venkatachalapathi and G. M. Anantharamaiah},
  title = {The Amphipathic Helix in the Exchangeable Apolipoproteins: A Review
	of Secondary Structure and Function},
  journal = JLR,
  year = {1992},
  volume = {33},
  pages = {141--166}
}

@ARTICLE{SHIF92,
  author = {Mark A. Shifman and Andreas Windemuth and Klaus Schulten and Perry
	L. Miller},
  title = {Molecular Dynamics Simulation on a Network of Workstations Using
	a Machine-Indepen\-dent Parallel Programming Language},
  journal = CBR,
  year = {1992},
  volume = {25},
  pages = {168--180}
}

@BOOK{SIMM92,
  title = {Muscular Contraction},
  publisher = {Cambridge University Press},
  year = {1992},
  author = {Robert M. Simmons}
}

@ARTICLE{SiTW92,
  author = {J.C. Simo and N. Tarnow and K.K. Wong},
  title = {Exact energy-momentum conserving algorithms and symplectic schemes
	for nonlinear dynamics},
  journal = {Computer Methods in Appl. Mech. and Engin.},
  year = {1992},
  volume = {100},
  pages = {63--116}
}

@ARTICLE{SiTa92,
  author = {J. C. Simo and N. Tarnow},
  title = {The Discrete Energy-Momentum Method. {C}onserving Algorithms for
	Nonlinear Elastodynamics},
  journal = {ZAMP},
  year = {1992},
  volume = {43},
  pages = {757--793}
}

@TECHREPORT{SiTa92b,
  author = {J. C. Simo and N. Tarnow},
  title = {A Review of Conserving Algorithms for Nonlinear Dynamics},
  institution = {Dept.\ Mechanical Engineering, Stanford Univ.},
  year = {1992},
  number = {SUDAM Report 92-7},
  address = {California}
}

@ARTICLE{SIMO92,
  author = {S.A. Simon and T.J. Mcintosh and A.D. Magid and D. Needham},
  title = {Modulation of the interbilayer hydration pressure by the addition
	of dipoles at the hydrocarbon/water interface},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {786--799}
}

@ARTICLE{SIMP92,
  author = {Simonson, T. and Br{\"u}nger, A. T.},
  title = {Thermodynamics of Protein Peptide Interactions in the Ribonuclease-S
	System Studied by Molecular Dynamics and Free Energy Calculations},
  journal = {Biochemistry},
  year = {1992},
  volume = {31},
  pages = {8661--8674}
}

@ARTICLE{SkGe92,
  author = {R.~D. Skeel and C. W. Gear},
  title = {Does variable step size ruin a symplectic integrator?},
  journal = {Physica D},
  year = {1992},
  volume = {60},
  pages = {311--313}
}

@ARTICLE{SMIT92a,
  author = {Steven B. Smith and Laura Finzi and Carlos Bustamante},
  title = {Direct mechanical measurements of the elasticity of single {DNA}
	molecules by using magnetic beads},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {1122--1126}
}

@ARTICLE{SONG92,
  author = {M.~Y.~Song and M.~S.~Jhon},
  title = {Molecular dynamics study of the effect of ion concentration on the
	{B-DNA}, {Z-DNA} and {DNA}-daunomycin complex},
  journal = JMS,
  year = {92},
  volume = {257},
  pages = {33--47},
  annote = {condensed ion models, refs simulation by levitt of dodecamer, distance
	dependent dielectric, 12\AA cutoff, 1fs timestep, 300K, 100ps, not
	very good analysis}
}

@ARTICLE{SuWi92,
  author = {G.J. Sussman and J. Wisdom},
  title = {Chaotic evolution of the solar system},
  journal = SCI,
  year = {1992},
  volume = {257},
  pages = {56--62}
}

@ARTICLE{SWIN92,
  author = {N. V. Swindale},
  title = {A Model for the Coordinated Development of Columnar Systems in Primate
	Striate Cortex},
  journal = BC,
  year = {1992},
  volume = {66},
  pages = {217--230}
}

@ARTICLE{THER92,
  author = {J. A. Theriot and T. J. Mitchison and L. G. Tilney and D. A. Portnoi},
  title = {The rate of actin-based motility of intracellular {{\em Listeria
	monocytogenes}} equals the rate of actin polymerization},
  journal = NAT,
  year = {1992},
  volume = {357},
  pages = {257--260}
}

@ARTICLE{THOM92,
  author = {J. L. Thomas and D. A. Tirrell},
  title = {Polyelectrolyte-Sensitized Phospholipid Vesicles},
  journal = ACR,
  year = {1992},
  volume = {25},
  pages = {336--342},
  number = {8},
  address = {DA Tirrell, Univ Massachusetts, Dept Polymer Sci \& Engn, Amherst,
	MA 01003},
  annote = {requested Tx=19920925.},
  keywords = {MODEL MEMBRANE SYSTEMS; CIS-TRANS ISOMERIZATION; LIPID PHASE-TRANSITIONS;
	SYNTHETIC-POLYMERS; CELL- MEMBRANES; PHOSPHATIDYLETHANOLAMINE LIPOSOMES;
	STRUCTURAL REORGANIZATION; POLY(2-ETHYLACRYLIC ACID); BILAYER VESICLES;
	LIGHT-SCATTERING},
  publisher = {Amer Chemical Soc, 1155 Sixteenth Street N W, Washington, DC 20036}
}

@ARTICLE{THOM92A,
  author = {L. K. Thompson and A. E. {Mc}{Dermott} and J. Raap and C. M. {van
	der} Wielen and J. Lugtenburg and J. Herzfeld and R. G. Griffin},
  title = {Rotational Resonance {NMR} Study of the Active Site Structure in
	Bacteriorhodopsin: Conformation of the Schiff Base Linkage},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {7931--7938}
}

@ARTICLE{TREU91,
  author = {Herbert Treutlein and Klaus Schulten and Axel Br{\"u}nger and Martin
	Karplus and J. Deisenhofer and H. Michel},
  title = {Chromophore-Protein Interactions and the Function of the Photosynthetic
	Reaction Center: A Molecular Dynamics Study},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {75--79},
  tbtechrep = {TB-91-10}
}

@ARTICLE{TuBM92,
  author = {M.~Tuckerman and B.~J.~Berne and G.~J.~Martyna},
  title = {Reversible multiple time scale molecular dynamics},
  journal = JCP,
  year = {1992},
  volume = {97},
  pages = {1990--2001},
  number = {3},
  nremark = {the attribution to H.F. Trotter, AMS Proc. 10, p545 (1959), seems
	questionable, because Trotter does not seem to give the second order
	symmetric splitting; rather he gives a first order splitting and
	uses it only for theoretical purposes}
}

@ARTICLE{ULRI92A,
  author = {A. S. Ulrich and M. P. Heyn and A. Watts},
  title = {Structure Determination of the Cyclohexene Ring of Retinal in Bacteriorhodopsin
	by Solid-State Deuterium {NMR}},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {10390--10399}
}

@INCOLLECTION{ULRI92,
  author = {A. S. Ulrich and I. Wallat and M. P. Heyn and A. Watts},
  title = {Evidence for a Curved Retinal in {BR} From Solid-State $^2${H-NMR}},
  booktitle = {Structures and Functions of Retinal Proteins},
  publisher = {Colloque {INSERM} / John Libbey Eurotext Ltd.},
  year = {1992},
  editor = {J. L. Rigaud},
  volume = {221},
  pages = {247--249}
}

@ARTICLE{VARO92,
  author = {G. V\'{a}r\'{o} and L. Zimanyi and M. Chang and B. F. Ni and R. Needleman
	and J. K. Lanyi},
  title = {A Residue Substitution near the $\beta$-Ionone Ring of the Retinal
	Affects the {M} Substates of Bacteriorhodopsin},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {820--826}
}

@ARTICLE{WETE92,
  author = {M. {Van de Wetering} and H. Clevers},
  title = {Sequence-specific interaction of the {HMG} box domain proteins {TCF-1}
	and {SRY} within the minor groove of a {Watson-Crick} double helix},
  journal = EMBO,
  year = {1992},
  volume = {11},
  pages = {3039--3044},
  number = {8}
}

@ARTICLE{VANG92,
  author = {G. Vanginkel and J. M. Muller and F. Siemsen and A. A. Vantveld and
	L. J. Korstanje and M. A. M. Vanzandvoort and M. L. Wratten and A.
	Sevanian},
  title = {Impact of Oxidized Lipids and Antioxidants, Such as Vitamin E and
	Lazaroids, on the Structure and Dynamics of Unsaturated Membranes},
  journal = JCS # { - Faraday Transactions},
  year = {1992},
  volume = {88},
  pages = {1901--1912},
  number = {13},
  address = {G Vanginkel, Univ Utrecht, Dept Molec Biophys, Buys Ballot Lab, Princetonplein
	5, 3584 CC Utrecht, Netherlands},
  annote = {requested Tx=19920901.; via interlibrary loan},
  keywords = {TRANSITION-MOMENT DIRECTIONS; ELECTRON-SPIN-RESONANCE; SLOW-MOTION
	ESR; ALPHA-TOCOPHEROL; MODEL MEMBRANES; POLARIZED FLUORESCENCE; REORIENTATIONAL
	DYNAMICS; PLANAR MULTIBILAYERS; MAGNETIC-RESONANCE; RAT-LIVER}
}

@ARTICLE{VENA92,
  author = {Richard M.~Venable and G\"oran Widmalm and Bernard R.~Brooks and
	William Egan and Richard W. Pastor},
  title = {Conformational States of a {\sc TT} Mismatch from Molecular Dynamics
	Simulation of Duplex d({\sc CGCGATTCGCG}) },
  journal = {Biopolymers},
  year = {1992},
  volume = {32},
  pages = {783--794},
  annote = {500ps traj of {DNA}in water}
}

@ARTICLE{VOLO92,
  author = {A. V. Vologodskii and S. D. Levene and K. V. Klenin and M. D. {Frank-Kamenetskii}
	and N. R. Cozzarelli},
  title = {Conformational and thermodynamic properties of supercoiled {DNA}},
  journal = JMB,
  year = {1992},
  volume = {227},
  pages = {1224--1243}
}

@ARTICLE{VoGS92,
  author = {Y. Vorobjev and X. Grant and H. A. Scheraga},
  title = {A Combined Iterative and Boundary Element Approach for Solution of
	the Non-Linear {P}oisson-{B}oltzmann Equation},
  journal = {J. Am.\ Chem.\ Soc.},
  year = {1992},
  volume = {114},
  pages = {3189--3196}
}

@ARTICLE{VOS92,
  author = {M.~H. Vos and J.~C. Lambry and S.~J. Robles and D.~C. Youvan and
	J.~Breton and J.~L. Martin},
  title = {Femtosecond spectral evolution of the excited state of bacterial
	reaction center at 10 K},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {613--617}
}

@ARTICLE{WAGN92,
  author = {C. R. Wagner and K. Hamana and S. C. R. Elgin},
  title = {A High-Mobility-Group protein and its {cDNAs} from {{\em Drosophila
	melanogaster}}},
  journal = {Mol. Cell. Biol.},
  year = {1992},
  volume = {12},
  pages = {1915--1923},
  number = {5}
}

@MANUAL{WALT92,
  title = {Babel Version 1.1},
  author = {P. Walters and M. Stahl},
  organization = {University of Arizona},
  address = {Tuscon, AZ},
  year = {1992},
  key = {BABEL}
}

@ARTICLE{WARS92,
  author = {A. Warshel},
  title = {Computer Simulation of Enzymatic Reactions.},
  journal = COSB,
  year = {1992},
  volume = {2},
  pages = {230--236}
}

@INCOLLECTION{WEIN92,
  author = {H. Weinstein and E. L. Mehler},
  title = {Structural Specificity in the Engineering of Biological Function:
	{I}nsights from the Dynamics of Calmodulin},
  booktitle = {Molecular Aspects of Biotechnology: Computational Models and Theories},
  publisher = {Kluwer Academic Publishers},
  year = {1992},
  editor = {J. Bertran},
  pages = {153--173},
  address = {Dordrecht, The Netherlands}
}

@ARTICLE{WHIT92,
  author = {Judith M. White},
  title = {Membrane Fusion},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {936--942}
}

@ARTICLE{WIEN92,
  author = {Michael C. Wiener and Stephen H. White},
  title = {Structure of a fluid dioleoylphosphatidylcholine bilayer determined
	by joint refinement of x-ray and neutron diffraction data; {I{}I}.
	Distribution and packing of terminal methyl groups},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {428--433},
  annote = {methylene volume=27+-1 A^3; methyl volume=57.2+-3.6 A^3; CH3 distributed
	with Gaussian function; many good refs; many good exp. data; average
	lipid cross-sectional area=59.3+-0.7 A^2; T=23K; area/head=60 A^2;
	larger area/head means higher hydration; molecular packing of chains
	is equivalent to that of liquid alkanes; good ideas on values to
	compare with simulation},
  key = {WienerB},
  keywords = {DOPC; fluid bilayer: L_\alpha phase; liquid crystal}
}

@ARTICLE{WIEN92A,
  author = {Michael C. Wiener and Stephen H. White},
  title = {Structure of a fluid dioleoylphosphatidylcholine bilayer determined
	by joint refinement of x-ray and neutron diffraction data; {I{}I{}I}.
	Complete structure},
  journal = BJ,
  year = {1992},
  volume = {61},
  pages = {434--447},
  annote = {excellent paper with many good ideas on values to compare with our
	simulation; 5.36=_.08 H2O/lipid in L_\alpha phase; exposure time
	24h...120h; lamellar repeat=49.1+-0.3A; RH=relative humidity; undulations
	of the membrane do not contribute significantly to width of distribution
	of quasimolecular parts; P-N distance=4.5A, headgroup angle=22+-4
	\degree resp. to bilayer surface (tilt angle); volume of DOPC molecule=1295A^3;
	average cross-sectional area/lipid=59.4A^2; surface area/lipid in
	crystalline all-trans state is 40A^2; for DOPC the surface area/lipid=60A^2
	and the thickness decreases to 27A; bilayer thickness here: PO4-PO4=40.3A},
  key = {WienerC},
  keywords = {DOPC; fluid bilayer: L_\alpha phase; liquid crystal; dynamic bilayer
	thickness; membrane; transbilayer thermal motion},
  suggestions = {compute mobilities (B factors) and see if the glycerol backbone is
	the most rigid part}
}

@ARTICLE{WiHo92b,
  author = {J. Wisdom and Holman},
  title = {Stability analysis of maps},
  year = {1992}
}

@ARTICLE{WiHo92a,
  author = {Jack Wisdom and Matthew Holman},
  title = {Symplectic Maps for the $n$-Body Problem: Stability Analysis},
  journal = {Astr.\ J.},
  year = {1992},
  volume = {104},
  pages = {2022--2029},
  number = {5},
  nremark = {WiHT96 say, ``Analysis of the mapping {H}amiltonian with techniques
	from non-linear dynamics (most notably the resonance overlap criteria)
	allow stability criteria to be developed for the integration algorithms
	(Wisdom and Holman, 1992)''}
}

@ARTICLE{WITH92,
  author = {J.~M.~Withka and S.~Swaminathan and J.~Srinivasan and D.~L.~Beveridge
	and P.~H.~Bolton.},
  title = {Water molecules in {DNA} recognition II: a molecular dynamics view
	of the structure and hydration of the {\em trp} operator},
  journal = SCI,
  year = {1992},
  volume = {255},
  pages = {597--599}
}

@ARTICLE{XIAN92,
  author = {T. X. Xiang and X. Chen and D. Anderson},
  title = {Transport methods for probing the barrier domain of lipid bilayer
	membranes},
  journal = BJ,
  year = {1992},
  volume = {63},
  pages = {78--88},
  annote = { Calculated permeability of acetamide across lipid bilayer, and is
	shown to be independent of bilayer thickness (?). They suggest that
	solvent domain only contributes slightly to the overall barrier.
	The contribution of a OH group was estimated to be 3.9 kcal/mol,
	showing the bilayer does not resemble octonal but is more polar than
	a hydrocarbon solvent.}
}

@INCOLLECTION{XU92,
  author = {Dong Xu and Klaus Schulten},
  title = {Multi-Mode Coupling of Protein Motion to Electron Transfer in the
	Photosynthetic Reaction Center: Spin-Boson Theory Based on a Classical
	Molecular Dynamics Simulation},
  booktitle = {The Photosynthetic Bacterial Reaction Center: II.\ Struc\-ture, Spectroscopy
	and Dynamics},
  publisher = {Plenum Press},
  year = {1992},
  editor = {J. Breton and A. Vermeglio},
  series = NATOA,
  pages = {301--312},
  address = {New York},
  tbtechrep = {TB-92-14}
}

@ARTICLE{YANG92,
  author = {Y. Yang and I. Tobias and W.K. Olson},
  title = {Finite element analysis of {DNA} supercoiling},
  journal = JCP,
  year = {1992},
  volume = {98},
  pages = {1673--1686}
}

@ARTICLE{YORK92,
  author = {D.~M.~York and T.~Darden and D.~Deerfield {II}},
  title = {The Interaction of {Na(I)}, {Ca(II)}, and {Mg(II)} Metal Ions with
	Duplex {DNA}: A Theoretical Modeling Study},
  journal = IJQCS,
  year = {1992},
  volume = {19},
  pages = {145--166},
  annote = {three 50ps MD studies, with water and ions, evals the ion/water interactions,
	result NA and Ca coordinate phos directly MG is hydrated}
}

@ARTICLE{YPHY92,
  author = {S.~K.~Yoshinaga and C.~L.~Peterson and I.~Herskowitz and K.~R.~Yamamoto},
  title = {Roles of {SW}l1, {SW}l2, and {SW}l3 Proteins for Transcriptional
	Enhancement by Steroid Receptors},
  journal = SCI,
  year = {1992},
  volume = {258},
  pages = {1598--1604},
  annote = {additional proteins required in GR activation}
}

@ARTICLE{YURK92,
  author = {Bernard Yurke and David Stoler},
  title = {Einstein-Podolsky-Rosen Effect from Independent Particle Sources},
  journal = PRL,
  year = {1992},
  volume = {68},
  pages = {1251--1254},
  number = {9}
}

@ARTICLE{ZAMA92,
  author = {Guido J.R. Zaman and Anita M. Kaan and John C.G. Schoenmakers},
  title = {Gene {V} protein-mediated translational regulation of the synthesis
	of gene {II} protein of the filamentous bacteriophage {M13}: a dispensable
	function of the filamentous-phage genome},
  journal = {J. Bacteriol.},
  year = {1992},
  volume = {174},
  pages = {595--600}
}

@ARTICLE{ZAWI92,
  author = {J. B. Zawilska and J. Z. Nowak},
  title = {Commentary-Regulatory Mechanisms in Melatonin Biosynthesis in Retina},
  journal = {Neurochem. Int.},
  year = {1992},
  volume = {20},
  pages = {23--36},
  number = {1}
}

@ARTICLE{ZHAN92,
  author = {Z. P. Zhang and M. J. Zuckermann and O. G. Mouritsen},
  title = {Effect of Intermonolayer Coupling on the Phase Behavior of Lipid
	Bilayers},
  journal = PRA,
  year = {1992},
  volume = {46},
  pages = {6707--6713},
  number = {10},
  address = {mcgill univ,ctr phys mat,dept phys,3600 univ st, montreal h3a 2t8,
	quebec, canada. tech univ denmark,dept phys chem, dk-2800 lyngby,
	denmark. tech univ denmark,canadian inst adv res, dk-2800 lyngby,
	denmark. canada. denmark.},
  annote = {A statistical-mechanical lattice model is proposed to describe the
	acyl-chain main phase transition in a hydrated lipid bilayer. The
	model is built on a two-dimensional multistate lattice model to describe
	the intramonolayer interactions within the two separate lipid monolayers
	of the bilayer. The coupling between the two monolayers is modeled
	both indirectly by hydrophobic acyl-chain mismatch interactions that
	ensure compatibility between the two monolayers, and by a direct
	intermonolayer attractive dispersion force. The nature of the phase
	transition is studied by computer-simulation methods involving standard
	{M}onte {C}arlo simulation, as well as the extrapolation method of
	Ferrenberg and Swendsen `Phys. Rev. Lett. 61, 2635 (1988) and the
	Lee-Kosterlitz technique `Phys. Rev. Lett. 65, 137 (1990); Phys.
	Rev. B 43, 3265 (1991) . It is found that the absence of a phase
	transition in a set of uncoupled monolayers is restored by a weak
	intermonolayer interaction. The bilayer properties in the transition
	region are described with particular emphasis on the lateral density
	fluctuations and the resulting dynamic bilayer heterogeneity. The
	theoretical results are discussed in relation to experimental data.
	requested Tx=19930108.},
  keywords = {phospholipid-bilayers. membranes. transitions. fluctuations. simulation.
	model}
}

@ARTICLE{ZHEN92,
  author = {C. Zheng and G. Vanderkooi },
  title = {Molecular Origin of the internal dipole potential in lipid bilayers:
	calculation of the electrostatic potential},
  journal = {Biophys. J},
  year = {1992},
  volume = {63},
  pages = {935--941}
}

@ARTICLE{ZHUK92,
  author = {E.~A. Zhukovsky and P.~R. Robinson and D.~D. Oparin},
  title = {Changing the Location of the Schiff Base Counterion in Rhodopsin},
  journal = BCH,
  year = {1992},
  volume = {31},
  pages = {10400--10405}
}

@INPROCEEDINGS{ZILK92,
  author = {A. Zilker and H. Strey and Erich Sackmann},
  title = {Erythrocytes Membranes: Tethered Shells with Fluid-like Deformation
	Regime},
  booktitle = {The Structure and Conformation of Amphiphilic Membranes},
  year = {1992},
  editor = {R. Lipowski and D. Richter and K. Kremer},
  volume = {66},
  series = {Springer Proceedings in Physics},
  pages = {113--127},
  address = {Berlin, Heidelberg},
  publisher = {Springer}
}

@ARTICLE{ZILK92A,
  author = {A. Zilker and M. Ziegler and Erich Sackmann},
  title = {Spectral Analysis of Erythrocyte Flickering in the {0.3-4-MU-M-1}
	Regime by Microinterferometry Combined with fast Image Processing},
  journal = PRA,
  year = {1992},
  volume = {46},
  pages = {7998--8002},
  number = {12},
  abstract = {Reflection interference microscopy in combination with real-time image
	processing was applied to determine the spatial spectrum of the mean-square
	amplitude of erythrocyte flickering in the wave-vector regime 0.3
	less-than-or-equal-to q less-than-or-equal-to 4 mum-1. The mean-square
	amplitude scales as q4+/-e for q greater-than-or-equal-to 0.7 mum-1,
	suggesting that flickering is dominated mainly by bending stiffness.
	We measured a bending modulus of K(c) = (2 +/- 0.5) x 10(-20) N m
	as compared to K(c) = (5 +/- 1.5) x 10(-20) N m found for dimyristoylphosphatidylcholine
	(DMPC) vesicles with the same technique.},
  address = {TECH UNIV MUNICH,DEPT PHYS E22,BIOPHYS GRP, W-8046 GARCHING, GERMANY.},
  annote = {requested Tx=19930206.},
  keywords = {elastic-moduli. membranes. fluctuations. shape.}
}

@ARTICLE{ZILL92,
  author = {J.~Zilliacus and A.~Wright and U. Norinder and J.~Gustafsson and
	J.~Carlstedt-Duke },
  title = {Determinants for {DNA}--binding site recognition by the glucocorticoid
	receptor.},
  journal = JBC,
  year = {1992},
  volume = {267},
  pages = {24941--24947},
  annote = {experimental study showing that not only the P-box residues are involved
	in binding specificity}
}

@ARTICLE{ZIMA92,
  author = {L. Zim\'{a}nyi and Y. Cao and M. Chang and B. Ni and R. Needleman
	and J. K. Lanyi},
  title = {The Two Consecutive {M} Substrates in the Photocycle of Bacteriorhodpsin
	are Affected Specifically by the {D85N} and {D96N} Residue Replacements},
  journal = PCPB,
  year = {1992},
  volume = {56},
  pages = {1049--1055}
}

@INPROCEEDINGS{PAUS91,
  author = {Randy Pausch},
  title = {Virtual Reality on Five Dollars a Day},
  year = {1991},
  month = APR,
  organization = {Proceedings of the ACM SIGCHI Human Factors in Computer Systems Conference},
  adress = {New Orleans},
  email = {Pausch@Virginia.edu},
  school = {University of Virginia, Computer Science Department,Thornton Hall,Charlottesville,
	VA 22903}
}

@INPROCEEDINGS{SUNT91,
  author = {J. P. E. Sunter and E. C. Koenders and A. W. P. Bakkers},
  title = {Post-Game Analysis on Transputers},
  booktitle = {{TRANSPUTING `91}},
  year = {1991},
  editor = {Peter Welch and Dyke Stiles and Tosiyasu L. Kunii and Andr{\'e} Bakkers},
  pages = {330--341},
  address = {Amsterdam},
  month = APR,
  publisher = {IOS Press},
  annote = {Proceedings of the World Transputer User Group (WOTUG) Conference
	22--26~April~1991 --- Sunnyvale, CA}
}

@INCOLLECTION{AKER91,
  author = {I.~E.~Akerblom and P.~L.~Mellon},
  title = {Repression of Gene Expression by Steroid and Thyroid Hormones},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {175--196}
}

@ARTICLE{AKUT91,
  author = {H. Akutsu and T. Nagamori},
  title = {Conformational analysis of the polar head group in phosphatidylcholine
	bilayers: a structural change induced by cations},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {4510--4516},
  annote = {requested Tx=19920908.; head group inclined by 18^o to surface of
	DPC in LC phase}
}

@ARTICLE{ALAM91,
  author = {T.~M.~Alam and J.~Orban and G.~P.~Drobny.},
  title = {Deuterium {NMR} investigation of backbone dynamics in the synthetic
	oligonucleotide {[d(CGCGAATTCGCG)]}2},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {9229--9237}
}

@ARTICLE{ANDE91,
  author = {P. O. Anderson and T. Gillbro and L. Ferguson and R. J. Cogdell},
  title = {Absorption spectral shifts of carotenoids related to medium polarizability},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {353--360}
}

@ARTICLE{AREN91,
  author = {G.~Arents and R.~W.~Burlingame and B.-C.~Wang and W.~E.~Love and
	E.~N.~Moudrianakis},
  title = {The nucleosomal core histone octamer at {3.1\,\AA} resolution: A
	tripartite protein assembly and a left-handed superhelix},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {10148--10152}
}

@ARTICLE{ARTU91,
  author = {P. Artursson and J. Karlsson},
  title = {Correlation between oral drug absorption in humans and apparent drug
	permeability coefficients in human intestinal epithelial {(CACO-2)}
	cells},
  journal = BBRC,
  year = {1991},
  volume = {175},
  pages = {880--885},
  annote = {Monolayers of a well differented human intestinal epithelial cell
	line, Caco-2, were used as a model to study passive drug absorption
	across the intestinal epithelium. The absortion in human are well
	correlated to the permeability measured in Caco-2 cell monolayer.}
}

@ARTICLE{AuFr91,
  author = {S. P. Auerbach and A. Friedman},
  title = {Long-Time Behaviour of Numerically Computed Orbits: Small and Intermediate
	Timestep Analysis of One-Dimensional Systems},
  journal = {J. Comput. Phys.},
  year = {1991},
  volume = {93},
  pages = {189--223}
}

@ARTICLE{AUGS91,
  author = {Joseph D. Augspurger and Clifford E. Dykstra and Eric Oldfield},
  title = {Correlation of Carbon-13 and Oxygen-17 Chemical Shifts and the Vibrational
	Frequency of Electrically Perturbed Carbon Monoxide: A Possible Model
	for Distal Ligand Effects in Carbonmonoxyheme Proteins},
  journal = JACS,
  year = {1991},
  volume = {113},
  pages = {2447--2451}
}

@ARTICLE{BALA91A,
  author = {S. P. Balashov and E. S. Imasheva and R. Govindjee and T. G. Ebrey},
  title = {Quantum Yield Ratio of the Forward and Back Light Reactions of Bacteriorhodopsin
	at Low Temperature and Photosteady-State Concentration of the Bathoproduct
	{K}},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {955--961}
}

@ARTICLE{BALA91,
  author = {S. P. Balashov and N. V. Karneyeva and F. F. Litvin and T. G. Ebrey},
  title = {Bathoproducts and Conformers of All-{\it trans}- and 13-{\it cis}-Bacteriorhodopsin
	at 90 K},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {949--953}
}

@INCOLLECTION{BaBr91,
  author = {Dinshaw S. Balsara and Achi Brandt},
  title = {Multilevel Methods for Fast Solution of {N}-Body and Hybrid Systems},
  booktitle = {International Series of Numerical Mathematics},
  publisher = {Birkh\"auser Verlag},
  year = {1991},
  volume = {98},
  pages = {131--142},
  address = {Basel}
}

@ARTICLE{BaSh91,
  author = {Andr{\'e} D. Bandrauk and Hai Shen},
  title = {Improved Exponential Split Operator Method for Solving the Time-Dependent
	{S}chr{\"o}dinger Equation},
  journal = {Chem.\ Phys.\ Lett.},
  year = {1991},
  volume = {176},
  pages = {428--432},
  number = {5},
  nremark = {suzu: hi order decomp of exp ops will be useful in molecular physics}
}

@TECHREPORT{BANK91,
  author = {Brad Banko and Helmut Heller},
  title = {User Manual for {EGO} --- {R}elease 1.1},
  institution = {University of Illinois},
  year = {1991},
  type = {Beckman Institute Technical Report},
  number = {TB-92-07},
  tbtechrep = {TB-92-07}
}

@MANUAL{BANK91-LONG,
  title = {User Manual for {EGO} --- {R}elease 1.1},
  author = {Brad Banko and Helmut Heller},
  organization = {Theoretical Biophysics Group at the University of Illinois at Urbana-Champaign,
	Beckman Institute},
  address = {405~N.~Mathews Ave., Urbana, IL~61801, U.S.A.},
  year = {1991},
  note = {[Beckman Institute Technical Report TB-92-07]},
  tbtechrep = {TB-92-07}
}

@CONFERENCE{BARS91D,
  author = {Daniel Barsky and Benno P{\"u}tz and Klaus Schulten and Richard L.
	Magin},
  title = {Theory of Compartmentalized Contrast Agents: Improved Contrast for
	Microscopic MRI},
  booktitle = {Tenth Annual Scientific Meeting and Exhibition, Works in Progress},
  year = {1991},
  pages = {1183},
  publisher = {Society of Magnetic Resonance in Medicine, Inc.}
}

@ARTICLE{BART91,
  author = {G.J. Barton and R.H. Newman and P.S. Freemont and M.J. Crumpton},
  title = {Amino acid sequence analysis of the annexin super-gene family of
	proteins},
  journal = {Eur.\ J.\ Biochem.},
  year = {1991},
  volume = {198},
  pages = {749--760}
}

@ARTICLE{BAYL91,
  author = {S. B. Baylin and M. Makos and J. Wu and R.-W. C. Yen and A. de Bustros
	and P. Vertino and B. D. Nelkin},
  title = {Abnormal Patterns of {DNA} Methylation in Human Neoplasia: Potential
	Consequences for Tumor Progression},
  journal = {Cancer Cells},
  year = {1991},
  volume = {3},
  pages = {383--389},
  number = {10}
}

@INCOLLECTION{BEAT91,
  author = {M.~Beato and D.~Barettino and U.~Br{\"u}ggemeier and G.~Chalepakis
	and R.~J.~G.~Hach{\'e} and M.~Kalffe and B.~Pi{\~n}a and M.~Schauer
	and E.~P.~Slater and M.~Truss},
  title = {Characterization of {DNA} Receptor Interactions},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {197--216}
}

@ARTICLE{BECH91,
  author = {B. Bechinger and Joachim Seelig},
  title = {Conformational changes of the phosphatidylcholine headgroup due to
	membrane dehydration. A {$^2$H-NMR} study},
  journal = CPLI,
  year = {1991},
  volume = {58},
  pages = {1--5},
  keywords = {D-{NMR}; P31-{NMR}; lipid hydration; lipid headgroup; model membranes;
	phosphocholine dipole; experimental; membrane; POPC; hydrogen bonding},
  suggestions = {look at headgroup orientation in different hydration states}
}

@ARTICLE{BECH91A,
  author = {Burkhard Bechinger and Joachim Seelig},
  title = {Interaction of Electric Dipoles with Phospholipid Headgroups. A {$^2$H}
	and {$^{31}$P {NMR}} Study of Phloretin and Phloretin Analogues in
	Phosphatidylcholine Membranes},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {3923--3929},
  keywords = {POPC; experimental; membrane; headgroup; hydration; electric charge;
	dipole; membrane potential},
  suggestions = {compute membrane potential}
}

@ARTICLE{BEIS91,
  author = {C. J. Beischel and V. Mani and R. Govindjee and T. G. Ebrey and D.
	R. Knapp and R. K. Crouch},
  title = {Ring Oxidized Retinals Form Unusual Bacteriorhodopsin Analogue Pigments},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {997--983}
}

@INCOLLECTION{BERK91,
  author = {Stanislav G. Berkovitch and Philippe Dalger and Ted Hesselroth and
	Thomas Martinetz and Beno{\^{\i}}t No{\"e}l and J{\"o}rg A. Walter
	and Klaus Schulten},
  title = {Vector Quantization Algorithm for Time Series Prediction and Visuo-Motor
	Control of Robots},
  booktitle = {{Verteilte K\"unstliche Intelligenz und kooperatives Arbeiten}},
  publisher = {Springer},
  year = {1991},
  editor = {W. Brauer and D. Hernandez},
  volume = {291},
  series = {Informatikfachberichte},
  pages = {443--447},
  address = {Berlin}
}

@ARTICLE{BERK91A,
  author = {Max L. Berkowitz and K. Raghavan},
  title = {Computer simulation of a water/membrane interface},
  journal = LM,
  year = {1991},
  volume = {7},
  pages = {1042},
  annote = {32 lipids; 437 water molecules; T=285K; PO4-PO4 distance is 16\AA
	filled with water; periodic boundary; gel phase (hydrocarbon chains
	were fixed); AMBER; 2*100ps runs; next neighbor of water if distance
	<=3.3\AA; h-bond present if angle (OH-OO)<=35^o; they observe dip
	in the water density profile; thermal motion does not smoothe out
	polarization oscillations; perhaps hydrogen bond deficiency could
	be responsible for hydration force},
  keywords = {hydration force; DLPE; water ordering in head group region}
}

@ARTICLE{BIRG91A,
  author = {R. R. Birge and T. M. Cooper and A. F. Lawrence and M. B. Masthay
	and C.-F. Zhang and R. Zidovetzki},
  title = {Revised Assignment of Energy Storage in the Primary Photochemical
	Event in Bacteriorhodopsin},
  journal = JACS,
  year = {1991},
  volume = {113},
  pages = {4327}
}

@ARTICLE{BIRG91,
  author = {R. R. Birge and C. Zhang},
  title = {Two-Photon Double Resonance Spectroscopy of Bacteriorhodopsin. Assignment
	of the Electronic and Dipolar Properties of the Low-Lying {$^1$A${^{*-}}{_g}$-like}
	and {$^1$B${^{*+}}{_u}$-like} $\pi,\pi^*$ States.},
  journal = JCP,
  year = {1991},
  volume = UNKNOWN,
  annote = {In press at some time, should check if it has been published.}
}

@PHDTHESIS{BJOR91,
  author = {R. D. Bjornson},
  title = {Linda on Distributed Memory Multiprocessors},
  school = {Yale University, Dept.\ of Comp.\ Sci.},
  year = {1991},
  address = {New Haven, CT}
}

@ARTICLE{BOEH91,
  author = {Klaus Boehncke and Marco Nonella and Klaus Schulten and Andrew {H.-J.}
	Wang},
  title = {Molecular Dynamics Investigation of the Interaction Between {DNA}
	and Dystamycin},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {5465--5475}
}

@INPROCEEDINGS{BOHR91,
  author = {H. G. Bohr and P. G. Wolynes},
  title = {Protein Folding: A Physical View of Neural Network Approaches},
  booktitle = {Proceedings of Workshop on Neural Networks: From Biology to High
	Energy Physics},
  year = {1991},
  address = {Marciana Marina, Elba, Italy},
  note = {In press}
}

@BOOK{BRAN91A,
  title = {Introduction to Protein Structure},
  publisher = {Garland Publishing, Inc.},
  year = {1991},
  author = {C. Branden and J. Tooze},
  address = {New York and London}
}

@BOOK{BrTo91,
  title = {Introduction to Protein Structure},
  publisher = {Addison Wesley Publishing Inc.},
  year = {1991},
  author = {C. Branden and J. Tooze}
}

@INPROCEEDINGS{BRAN91,
  author = {A. Brandt},
  title = {Multilevel computations of integral transforms and particle interactions
	with oscillatory kernels},
  booktitle = {Proc.\ IMACS 1st Int.\ Conf.\ on Comp.\ Phys.},
  year = {1991},
  address = {Boulder, CO}
}

@ARTICLE{Bran91b,
  author = {A. Brandt},
  title = {Multilevel computations of integral transforms and particle interactions
	with oscillatory kernels},
  journal = cpc,
  year = {1991},
  volume = {65},
  pages = {24--38},
  number = {1-3},
  abstract = {After a brief overview of multilevel computations in general, algorithms
	for performing dense-matrix multiplication are described for n x
	n matrices representing the interaction of n particles or the discretization
	of integral transforms on n gridpoints. For general asymptotically
	smooth kernels, possibly multiplied by an oscillatory exponential,
	the matrix multiplication can be performed in O(n(log n)q) operations,
	where q depends on the type of the kernel, the underlying spatial
	dimension, and the relation required between n and the accuracy of
	the calculation. Relations to, and combination with, Fourier methods
	are delineated.},
  address = {Boulder, CO},
  booktitle = {Proc.\ IMACS 1st Int.\ Conf.\ on Comp.\ Phys.}
}

@ARTICLE{BREN91,
  author = {M. Brenneman and S. W. Chiu and E. Jakobsson},
  title = {Computational studies on the side chain conformations of gramicidin},
  journal = ABJ,
  year = {1991},
  volume = {59},
  number = {320a},
  annote = {ridiculous: this is just the abstract to a poster!}
}

@ARTICLE{BRUN91,
  author = {J. Brunet and J. P. Mesirov and A. Edelman},
  title = {An Optimal Hypercube Direct {N}-body Solver on the {Connection Machine}},
  journal = {Proceedings of Supercomputing~'90},
  year = {1991}
}

@ARTICLE{BRUN91B,
  author = {A. Br{\"u}nger},
  title = {Simulated Annealing in Crystallography},
  journal = ARP,
  year = {1991},
  volume = {42},
  pages = {197--223}
}

@ARTICLE{BAUE91B,
  author = {Hans-Dieter B{\"a}uerle and Joachim Seelig},
  title = {Interaction of Charged and Uncharged Calcium Channel Antagonists
	with Phospholipid Membranes. Binding Equilibrium, Binding Enthalpy,
	and Membrane Location},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7203--7211},
  keywords = {membrane; experimental; POPC}
}

@ARTICLE{BULD91,
  author = {G. B{\"u}ldt and K. Konno and K. Nakanishi and H. Pl{\"o}hn and B.
	N. Rao and N. A. Dencher},
  title = {Heavy-Atom Labelled Retinal Analogues Located in Bacteriorhodopsin
	by X-Ray Diffraction},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {873--879}
}

@TECHREPORT{CaSa91,
  author = {M. P. Calvo and J. M. Sanz-Serna},
  title = {Variable Steps for Sympletic Integrators},
  institution = {Departamento de Matematica Aplicada y Computaci\'on, Universidad
	de Valladolid},
  year = {1991},
  number = {1991/3},
  address = {Valladolid, Spain}
}

@ARTICLE{CaRo91,
  author = {J. Candy and W. Rozmus},
  title = {A Symplectic Integration Algorithm for Separable \mbox{Hamiltonian}
	Functions},
  journal = {J. Comput. Phys.},
  year = {1991},
  volume = {92},
  pages = {230--256}
}

@ARTICLE{CAO91,
  author = {Y. Cao and G. V{\'a}r{\'o} and M. Chang and B. Ni and R. Needleman
	and J. K. Lanyi},
  title = {Water Is Required for Proton Transfer from Aspartate-96 to the Bacteriorhodopsin
	{Schiff} Base},
  journal = BCH,
  year = {1991},
  volume = {74},
  pages = {10972--10979}
}

@ARTICLE{CARL91,
  author = {L. Carlacci and M. W. Schulz and K. C. Chou},
  title = {Geometric and Energy Parameters in Lysine-Retinal Chromophores},
  journal = PE,
  year = {1991},
  volume = {4},
  pages = {885--889}
}

@ARTICLE{CARL91A,
  author = {M.-F. Carlier},
  title = {Actin: Protein Structure and Filament Dynamics},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {1--4}
}

@ARTICLE{CARS91,
  author = {M. Carson},
  title = {{RIBBONS} 2.0},
  journal = JAC,
  year = {1991},
  volume = {24},
  pages = {958--961}
}

@ARTICLE{CART91,
  author = {Bo Cartling},
  title = {Stochastic Model of Intermode Couplings in Protein Dynamics},
  journal = JCP,
  year = {1991},
  volume = {94},
  pages = {6203--6210}
}

@ARTICLE{CEVC91,
  author = {Gregor Cevc},
  title = {Hydration force and the interfacial structure of the polar surface},
  journal = JCS # { - Faraday Transactions},
  year = {1991},
  volume = {87},
  pages = {2733--2739},
  annote = {requested Tx=19921024.}
}

@ARTICLE{CHAN91,
  author = {C. Chang and N. Sekiya and K. Yoshihara},
  title = {O-H Stretching Vibration in {Fourier} Transform Difference Infrared
	Spectra of Bacteriorhodopsin},
  journal = FEBS,
  year = {1991},
  volume = {287},
  pages = {157--159}
}

@ARTICLE{CHAR91,
  author = {H. Charibonneau and S. Kumar and J. P. Novack and D. K. Blumenthal
	and P. R. Griffin and J. Shabanowitz and D. F. Hunt and J. A. Beavo
	and K. A. Walsh},
  title = {Evidence for Domain Organization within the 61-k{Da} Calmodulin-Dependent
	Cyclic Nucleotide Phosphodiesterase},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7931--7940}
}

@ARTICLE{CHEN91,
  author = {W. Chen and M. S. Braiman},
  title = {Kinetic Analysis of Time-Resolved Infrared Difference Spectra of
	the {L} and {M} Intermediates of Bacteriorhodopsin},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {905--910}
}

@INCOLLECTION{CHIN91,
  author = {W.~W.~Chin},
  title = {Nuclear Thyroid Hormone Receptors},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {79--102}
}

@ARTICLE{CHIU91A,
  author = {S. W. Chiu and E. Jakobsson and S. Subramaniam and J. A. McCammon},
  title = {Time-correlation analysis of simulated water motion in flexible and
	rigid gramicidin channels},
  journal = {Biophys. J.},
  year = {1991},
  volume = {60},
  pages = {273--285},
  annote = {requested Tx=19920924.}
}

@ARTICLE{CHIU91B,
  author = {S. W. Chiu and L. Nicholson and M. T. Brenneman and S. Subramaniam
	and Q. Teng and C. North and J. A. McCammon and E. Jakobsson},
  title = {Molecular dynamics computations and solid state {NMR} of the gramicidin
	cation channel},
  journal = {Biophys. J.},
  year = {1991},
  note = {In press}
}

@ARTICLE{CHUR91,
  author = {Mair E. A. Churchill and Andrew A. Travers},
  title = {Protein motifs that recognize structural features of {DNA}},
  journal = TIBS,
  year = {1991},
  volume = {16},
  pages = {92--97}
}

@ARTICLE{CHYN91,
  author = {S. Chynoweth and U. C. Klomp and L. E. Scales},
  title = {Simulation of organic liquids using pseudo-pairwise interatomic forces
	on a toroidal transputer array},
  journal = CPC,
  year = {1991},
  volume = {62},
  pages = {297--306},
  annote = {reduces 3 and 4 body IA to pseudo 2 body IA; only short range IA
	up to 9\AA},
  keywords = {lubricants; domain decomposition; periodic boundaries}
}

@MISC{CLAR91,
  author = {Clark and T. W. and McCammon and J. A.},
  title = {Parallelization of a molecular dynamics non-bonded force algorithm
	for MIMD architecture, preprint},
  year = {1991}
}

@ARTICLE{COGN91,
  author = {J.~A.~H.~Cognet and Y.~Boulard and G.~V.~Fazakerley.},
  title = {Helical parameters, fluctuations, alternative hydrogen bonding, and
	bending in oligonucleotides containing a mismatched base-pair by
	{NOESY} distance restrained and distance free molecular dynamics},
  journal = JMB,
  year = {1991},
  volume = {246},
  pages = {209--226}
}

@ARTICLE{CRAV91,
  author = {C. J. Craven and G. S. Pawley},
  title = {Molecular dynamics of rigid polyatomic molecules on transputer arrays},
  journal = CPC,
  year = {1991},
  volume = {62},
  pages = {169--178},
  annote = {No full MD force field (only rigid body). Many small molecules. Stores
	all coordinates in each node, claims to gain high efficiency and
	good load balancing by this. Agrees that communication costs are
	neglectible. Compares to CRAY X-MP. A good paper. Did not cite~\cite{HELL90}}
}

@ARTICLE{CZEG91,
  author = {J. Cz{\'e}g{\'e} and L. Reinisch},
  title = {The {pH} Dependence of Transient Changes in the Curvature of the
	Purple Membrane},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {923--930}
}

@ARTICLE{DAGG91,
  author = {V. Daggett and M. Levitt},
  title = {A Molecular Dynamics Simulation of the {C}-Terminal Fragment of the
	{L7/L12} Ribosomal Protein in Solution},
  journal = CP,
  year = {1991},
  volume = {158},
  pages = {501--512}
}

@INCOLLECTION{DANI91,
  author = {M.~Danielsen},
  title = {Structure and Function of the Glucocorticoid Receptor},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {39--78}
}

@ARTICLE{DMLM91,
  author = {Malcolm E. Davis and Jeffrey D. Madura and Brock A. Luty and J. Andrew
	McCammon},
  title = {Electrostatics and Diffusion of Molecules in Solution: Simulations
	with the {U}niversity of {H}ouston {B}rownian Dynamics Program},
  journal = {Computer Phys.\ Comms.},
  year = {1991},
  volume = {62},
  pages = {187--197},
  nremark = {Paper about the implementation of UHBD}
}

@ARTICLE{DMSL91,
  author = {M. E. Davis and J. D. Madura and J. Sines and B. A. Luty and S. A.
	Allison and J. A. McCammon},
  title = {Diffusion-controlled enzymatic reactions},
  journal = {Methods Enzymol.},
  year = {1991},
  volume = {202},
  pages = {473--497}
}

@ARTICLE{DENC91,
  author = {N. A. Dencher and J. Heberle and C. Bark and M. H. J. Koch and G.
	Rapp and D. Oesterhelt and K. Bartels and G. B{\"u}ldt},
  title = {Proton Translocation and Conformational Changes During the Bacteriorhodopsin
	Photocycle: Time-Resolved Studies With Membrane-Bound Optical Probes
	and X-Ray Diffraction},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {881--887}
}

@ARTICLE{DENG91,
  author = {H. Deng and D. Manor and G. Weng and P. Rath and Y. Koutalos and
	T. Ebrey and R. Gebhard and J. Lugtenburg and M. Tsuda and R. H.
	Callender},
  title = {A Resonance Raman Study of Octopus Bathorhodopsin with Deuterium
	Labeled Retinal Chromophores},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {1001--1007}
}

@ARTICLE{DERG91,
  author = {F. Derguni and P. Mazur and K. Nakanishi and D. Starace and J. Saranak
	and K. Foster},
  title = {All-{\it trans}-{Retinal} is the Chromophore Bound to the Photoreceptor
	of the Alga},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1017--1021}
}

@ARTICLE{DiKG91,
  author = {H.-Q. Ding and N. Karasawa and W. A. {Goddard III}},
  title = {Million-Atom Simulations: Cell Multipole Method for Coulomb and London
	Nonbond Interactions},
  journal = {Bulletin of the American Physical Society},
  year = {1991},
  volume = {36},
  number = {6},
  booktitle = {Physics Computing'91},
  nremark = {taken from the ``Bulletin of the American Physical Society'', only
	the abstract was available. it might be in proceedings of the ``3rd
	International Conference on Computational Physics'', San Jose, CA,
	10--14~June, 1991},
  organization = {California Institute of Technology}
}

@ARTICLE{DING91,
  author = {H.-Q. Ding and N. Karasawa and W. A. {Goddard III}},
  title = {Million-Atom Simulations: Cell Multipole Method for Coulomb and London
	Nonbond Interactions},
  journal = {Bulletin of the American Physical Society},
  year = {1991},
  volume = {36},
  number = {6},
  anbooktitle = {Physics Computing'91},
  annote = {I took this from the ``Bulletin of the American Physical Society'',
	only the abstract was available. I hope there will be proceedings
	of the ``3rd International Conference on Computational Physics'',
	San Jose, CA, 10--14~June, 1991},
  anorganization = {California Institute of Technology}
}

@ARTICLE{DOIG91,
  author = {S. J. Doig and P. J. Reid and R. A. Mathies},
  title = {Picosecond Time-Resolved Resonance {Raman} Spectroscopy of Bacteriorhodopsin's
	{J}, {K}, and {KL} Intermediates},
  journal = JPC,
  year = {1991},
  volume = {95},
  pages = {6372--6379}
}

@ARTICLE{DOUG91,
  author = {Fred Douglis and John K. Ousterhout and M. Frans Kaashoek and Andrew
	S. Tanenbaum},
  title = {A Comparison of Two Distributed Systems: Amoeba and Sprite},
  journal = CSY,
  year = {1991},
  volume = {4},
  pages = {353--384},
  number = {4},
  keywords = {Amoeba; Sprite; Chorus; Mach}
}

@ARTICLE{DRAB91,
  author = {Wilfried Draber and Klaus Tietjen and Joachim F. Kluth and Achim
	Trebst},
  title = {Herbicides in Photosynthesis Research},
  journal = ACIEE,
  year = {1991},
  volume = {30},
  pages = {1621--1633},
  annote = {PS II is homolog to Rps.; good overview and introduction to photosynthesis
	research; good explanatory pictures},
  keywords = {photosystem II; Rps. viridis}
}

@ARTICLE{DUNL91,
  author = {P. V. Dunlap},
  title = {Organization and Regulation of Bacterial Luminescence Genes},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1157--1170}
}

@ARTICLE{DURU91,
  author = {J. Durup},
  title = {Protein Molecular Dynamics Constrained to Slow Modes. Theoretical
	Approach Based on a Hierarcy of Local Modes with a set of Holomonic
	Constraints: The method and its Test on Citrate Synthase},
  journal = JPC,
  year = {1991},
  volume = {95},
  pages = {1817--1829}
}

@ARTICLE{DER91,
  author = {A. D{\'e}r and S. Sz{\'a}raz and R. T{\'o}th-Bocon{\'a}di and Z.
	Tokaji and L. Keszthelyi and W. Stoeckenius},
  title = {Alternative Translocation of Protons and Halide Ions by Bacteriorhodopsin},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {4751--4755}
}

@ARTICLE{EDWA91,
  author = {S. F. Edwards and Moshe Schwartz},
  title = {Stochastic dynamics of a slightly deformed membrane},
  journal = PHYA,
  year = {1991},
  volume = {178},
  pages = {236--240},
  annote = {very mathematical, no simulations}
}

@ARTICLE{ERME91,
  author = {B. Ermentrout},
  title = {Stripes or Spots? {N}onlinear Effects in Bifurcation of Reaction-Diffusion
	Equations on the Square},
  journal = {Proc. R. Soc. Lond. A.},
  year = {1991},
  volume = {434},
  pages = {413--417}
}

@INCOLLECTION{ERWI91,
  author = {Edgar Erwin and Klaus Obermayer and Klaus Schulten},
  title = {Convergence Properties of Self-Organizing Maps},
  booktitle = {Artificial Neural Networks},
  publisher = {Elsevier},
  year = {1991},
  editor = {Teuvo Kohonen and Kai M{\"a}kisara and Olli Simula and Jari Kangas},
  pages = {409--414},
  address = {Amsterdam},
  tbtechrep = {TB-91-05}
}

@ARTICLE{EVAN91,
  author = {E. Evans and D. Berk and A. Leung},
  title = {Detachment of agglutinin-bonded red blood cells},
  journal = BJ,
  year = {1991},
  volume = {59},
  pages = {838--848}
}

@MANUAL{FELS91,
  title = {PHYLIB Manual Version 3.4},
  author = {J. Felsenstein},
  organization = {University Herbarium, University of California, Berkeley, CA},
  year = {1991}
}

@ARTICLE{FeWa91,
  author = {K. Feng and D.-L. Wang},
  title = {A note on conservation laws of symplectic difference schemes for
	{H}amiltonian systems},
  journal = {J.\ Comput.\ Math.},
  year = {1991},
  volume = {9},
  pages = {229--237}
}

@ARTICLE{FeWa91b,
  author = {K. Feng and D.-L. Wang},
  title = {Symplectic Difference Schemes for \mbox{Hamiltonian} Systems in General
	Symplectic Structure},
  journal = {J. Comput. Math.},
  year = {1991},
  volume = {9},
  pages = {86--96},
  number = {1}
}

@UNPUBLISHED{FENT91,
  author = {W. Fenton and B. Ramkumar and V. Saletore and A. Sinha and L. V.
	Kal{\'e}},
  title = {Supporting Machine Independent Programming on Diverse Parallel Architectures},
  note = {In press},
  year = {1991},
  journal = {Proc. of the International Conf.\ on Parallel Processing}
}

@ARTICLE{FERR91,
  author = {T. E. Ferrin and G. S. Couch and C. C. Huang and E. F. Pettersen
	and R. Langridge},
  title = {An Affordable Approach to Interactive Desktop Molecular Modeling},
  journal = JMG,
  year = {1991},
  volume = {9},
  pages = {27--32}
}

@ARTICLE{FISE91,
  author = {C. Richard Fisel and Jerome L. Ackerman and Richard B. Buxton and
	Leoncio Garrido and John W. Belliveau and Bruce R. Rosen and Thomas
	J. Brady},
  title = {MR Contrast Due to Microscopically Heterogeneous Magnetic Susceptibility:
	Numerical Simulations and Applications to Cerebral Physiology},
  journal = mrm,
  year = {1991},
  volume = {17},
  pages = {336--347}
}

@ARTICLE{FLAH91,
  author = {Kevin M. Flaherty and David McKay and Wolfgang Kabsch and Kenneth
	C. Holmes},
  title = {Similarity of the three-dimensional structures of actin and the {ATP}ase
	fragment of a 70-k{Da} heat shock cognate protein},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {5041--5045}
}

@ARTICLE{FORE91,
  author = {T.~R.~Forester and I.~R.~McDonald},
  title = {Molecular dynamics studies of the behaviour of water molecules and
	small ions in concentrated solutions of polymeric {B-DNA}.},
  journal = MP,
  year = {1991},
  volume = {72},
  pages = {643--660}
}

@ARTICLE{FOST91,
  author = {D.~Brian Foster and Douglas R.~Cavener and Fritz F.~Parl},
  title = {Binding analysis of the estrogen receptor to its specific {DNA} target
	site in human breast cancer},
  journal = {Cancer Research},
  year = {1991},
  volume = {51},
  pages = {3405--3410}
}

@ARTICLE{FrMc91,
  author = {P. O. Frederickson and O. A. McBryan},
  title = {Normalized Convergence Rates for the {PSMG} Method},
  journal = SJSSC,
  year = {1991},
  volume = {12},
  pages = {221--229},
  number = {1}
}

@ARTICLE{FRIE91A,
  author = {Friesner, R. A.},
  title = {New Methods for Electronic Structure Calculations on Large Molecules},
  journal = ARPC,
  year = {1991},
  volume = {42},
  pages = {341}
}

@ARTICLE{GALL91,
  author = {P. Galland},
  title = {Photosensory Adaptation in Aneural Organisms},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1119--1134}
}

@ARTICLE{GART91,
  author = {W. Gartner and D. Ullrich and K. Vogt},
  title = {QuantumYield of Chapso-Solubilized Rhodopsin and 3-hydroxy Retinal
	Containing Bovine Opsin},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1047--1055}
}

@ARTICLE{Ge91,
  author = {Z. Ge},
  title = {Equivariant symplectic difference schemes and generating functions},
  journal = {Physica D},
  year = {1991},
  volume = {49},
  pages = {376--386}
}

@ARTICLE{GHOM91,
  author = {F. Ghomashchi and B.-Z. Yu and O. Berg and M.K. Jain and M.H. Gelb},
  title = {Interfacial catalysis by phospholipase {A$_2$}: Substrate specificity
	in vesicles},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7318--7329},
  annote = {preference for negatively charged lipids}
}

@ARTICLE{GHOM91a,
  author = {F. Ghomashchi and B.-Z. Yu and E.D. Mihelich and M.K. Jain and M.H.
	Gelb},
  title = {Kinetic characterization of phospholipase {A$_2$} modified by monoalogue},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {9559--9569},
  annote = {monoalogue}
}

@ARTICLE{GIBS91,
  author = {N. J. Gibson and M. F. Brown},
  title = {Membrane Lipid Influences on the Energetics of the Metarhodopsin
	I and Metarhodopsin II Conformational States of Rhodopsin Probed
	by Flash Photolisis},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {985--992}
}

@ARTICLE{GIES91,
  author = {K. Giese and A. Amsterdam and R. Grosschedl},
  title = {{DNA}-binding properties of the {HMG} domain of the lymphoid-specific
	transcriptional regulator {LEF-1}},
  journal = {Genes and Development},
  year = {1991},
  volume = {5},
  pages = {2567--2578},
  number = {12b}
}

@ARTICLE{GlDC91,
  author = {B. Gladman and M. Duncan and J. Candy},
  title = {Symplectic Integrators for Long-Term Integrations in Celestial Mechanics},
  journal = {Celestial Mech. Dynamical. Astron.},
  year = {1991},
  volume = {52},
  pages = {221--240}
}

@ARTICLE{GOME91,
  author = {C. J. Gomer},
  title = {Preclinical Examination of First and Second Generation Photosensitizers
	used in Photodynamic Therapy},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1093--1107}
}

@BOOK{GREE91B,
  title = {Parallel Processing for Computer Graphics},
  publisher = {Pitman},
  year = {1991},
  author = {Stuart Green},
  address = {London},
  annote = {good description of SIMD, MIMD, etc.; historical overview of parallel
	computing; describes different machines and where they stem from:
	Transputer, Sequent, CM, GPP, iPSC, Cray; a good book},
  keywords = {ray tracing, hidden surface removal}
}

@INCOLLECTION{GREE91,
  author = {S.~Green and P.~Chambon},
  title = {The Oestrogen Receptor: From Perception to Mechanism},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {15--38}
}

@ARTICLE{GREE91C,
  author = {Duncan A. Greenhalgh and Christian Altenbach and Wayne L. Hubbell
	and H. Gobind Khorana},
  title = {Locations of {A}rg-82, {A}sp-85, and {A}sp-96 in helix C of bacteriorhodopsin
	relative to the aqueous boundaries},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {8626--8630}
}

@ARTICLE{GHWS91,
  author = {H. Grubm{\"u}ller and H. Heller and A. Windemuth and K. Schulten},
  title = {Generalized \mbox{Verlet} Algorithm for Efficient Molecular Dynamics
	Simulations with Long-Range Interactions},
  journal = {Molecular Simulation},
  year = {1991},
  volume = {6},
  pages = {121--142}
}

@ARTICLE{GRUB91,
  author = {Helmut Grubm{\"u}ller and Helmut Heller and Andreas Windemuth and
	Klaus Schulten},
  title = {Generalized {V}erlet Algorithm for Efficient Molecular Dynamics Simulations
	with Long-Range Interactions},
  journal = MS,
  year = {1991},
  volume = {6},
  pages = {121--142}
}

@ARTICLE{FRAU91,
  author = {H. Frauenfelder, S. G. Sligar, P. G. Wolynes},
  title = {The Energy Landscapes and Motions of Proteins},
  journal = SCI,
  year = {1991},
  volume = {254},
  pages = {1598--1603}
}

@INCOLLECTION{HAGE91,
  author = {G.~L.~Hager and T.~K.~Archer},
  title = {The Interaction of Steroid Receptors with Chromatin},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {217--231}
}

@ARTICLE{HAMM90,
  author = {Kenton D. Hammonds and Jean-Paul Ryckaert},
  title = {On the Convergence of the {SHAKE} Algorithm},
  journal = CPC,
  year = {1991},
  volume = {62},
  pages = {336--351},
  annote = {Do not use fictious bonds to constrain angles, but do use redundant
	bonds or redundant angles to constrain motions.}
}

@INPROCEEDINGS{HARA91,
  author = {S. Hara and H.W. Chang and K. Horigome and I. Kudo and K. Inoue},
  title = {Purification of mammalian nonpancreatic extracellular phospholipase
	{A$_2$}},
  booktitle = {Methods in enzymology},
  year = {1991},
  editor = {E. A. Dennis},
  pages = {381--389},
  address = {San Diego},
  publisher = {Academic Press}
}

@ARTICLE{HARR91,
  author = {S.~C.~Harrison},
  title = {A structural taxonomy of {DNA}--binding domains},
  journal = NAT,
  year = {1991},
  volume = {353},
  pages = {715--719},
  annote = {says that the zinc fingers in ER and GR are in fact type not zinc
	fingers but are class II zinc--binding motifs}
}

@ARTICLE{HaAv91,
  author = {R.~H. Hasse and V.~V. Avilov},
  title = {Structure and {M}andelung energy of spherical {C}oulomb crystals},
  journal = PRA,
  year = {1991},
  volume = {44},
  pages = {4506--4515},
  number = {7}
}

@INPROCEEDINGS{HAWT91,
  author = {A. M. Hawthornthwaite and R. J. Cogdell},
  title = {Bacteriochlorophyll binding proteins},
  booktitle = {Chlorophylls},
  year = {1991},
  editor = {H. Scheer},
  pages = {493--528},
  address = {Boca Raton},
  publisher = {CRC Press}
}

@ARTICLE{HERM91,
  author = {R. B. Hermann and E. Dow},
  title = {Construction of a Human Synovial Phospholipase~{A}$_2$ Model},
  journal = {Cray Channels},
  year = {1991},
  volume = {fall},
  pages = {2--5}
}

@BOOK{HERZ91,
  title = {Introduction to the Theory of Neural Computation},
  publisher = {Ad\-di\-son-Wesley},
  year = {1991},
  author = {John Hertz and Anders Krogh and Richard G. Palmer},
  address = {New York}
}

@ARTICLE{HEYN91,
  author = {M. P. Heyn and H. Otto},
  title = {Photoselection and Transient Linear Dichroism with Oriented Immobilized
	Purple Membranes: Evidence for Motion of the {C}(20)-Methyl Group
	of the Chromophore Towards the Cytoplasmic Side of the Membrane},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {1105--1112}
}

@ARTICLE{HILD91,
  author = {E. Hilderband and A. Schimz},
  title = {The Sensory Photoreceptors of {{\em Halobacterium halobium}} Revisted:
	Action Spectra and Influence of Background Light},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1027--1037}
}

@ARTICLE{HOLL91,
  author = {L. H. Holley and M. Karplus},
  title = {Neural networks for protein structure prediction},
  journal = {Methods in Enzymology},
  year = {1991},
  volume = {202},
  pages = {204}
}

@ARTICLE{HGS+92,
  author = {E. A. Holm and J. A. Glazier and D. J. Srolovitz and G. S. Grest},
  title = {Effects of lattice anisotropy and temperature on domain growth in
	the two-dimensional Potts model},
  journal = PRA,
  year = {1991},
  volume = {43},
  pages = {2662--2668}
}

@ARTICLE{HoGSG92,
  author = {E. A. Holm and J. A. Glazier and D. J. Srolovitz and G. S. Grest},
  title = {Effects of lattice anisotropy and temperature on domain growth in
	the two-dimensional Potts model},
  journal = PRA,
  year = {1991},
  volume = {43},
  pages = {2662--2668}
}

@ARTICLE{HOLM91,
  author = {Kenneth C. Holmes and Wolfgang Kabsch},
  title = {Muscle proteins: actin},
  journal = COSB,
  year = {1991},
  volume = {1},
  pages = {270--280}
}

@ARTICLE{HOUS91,
  author = {Catherine E. Houstis and Mokhtar Aboelaze},
  title = {A Comparative Performance Analysis of Mapping Applications to Parallel
	Multiprocessor Systems: A Case Study},
  journal = JPDC,
  year = {1991},
  volume = {13},
  pages = {17--29},
  annote = {control of a robot elbow manipulator},
  keywords = {Banyan network}
}

@ARTICLE{HU91,
  author = {Y. Hu and G. R. Fleming and Karl F. Freed and A. Perico},
  title = {Theory of long time protein dynamics: test of various reduced descriptions
	and role of internal variables},
  journal = CP,
  year = {1991},
  volume = {158},
  pages = {395}
}

@ARTICLE{HUBN91,
  author = {W. H{\"u}bner and H. H. Mantsch},
  title = {Orientation of specifically {$^{13}$C=O} labeled phosphatidylcholine
	multilayers from polarized attenuated total reflection {FT-IR} Spectroscopy},
  journal = BJ,
  year = {1991},
  volume = {59},
  pages = {1261--1272},
  annote = {requested Tx=19920908.}
}

@ARTICLE{IGLE91,
  author = {R.N. Iglesias-Prieto and N.S. Govind and R.K. Trench},
  title = {Apoprotein composition and spectroscopic characterization of the
	water-soluble peridinin-chlorophyll $a$-proteins from three symbiotic
	dinoflagellates},
  journal = PRSLB,
  year = {1991},
  volume = {246},
  pages = {275--283}
}

@ARTICLE{STRO91,
  author = {Robert E. Strout {II} and James R. McGraw and Alan C. Hindmarsh},
  title = {An Examination of the Conversion of Software to Multiprocessors},
  journal = JPDC,
  year = {1991},
  volume = {13},
  pages = {1--16},
  annote = {Data analysis is the first step: provide interdependencies of subroutine
	calls},
  keywords = {Cray X-MP/48; LSODE: linear equation solver}
}

@ARTICLE{ITO91,
  author = {Tomoyoshi Ito and others},
  title = {A Special-Purpose Computer for Gravitational Many-Body Systems: GRAPE-2},
  journal = {Publ. Astron. Soc. Japan},
  year = {1991},
  volume = {43},
  pages = {547}
}

@ARTICLE{JAIN91a,
  author = {M. K. Jain and G. Ranadive and B.-Z. Yu and H. M. Verheij},
  title = {Interfacial catalysis by phospholipase {A$_2$}: Monomeric enzyme
	is fully catalytically active at the bilayer interface},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7330--7340}
}

@ARTICLE{JAIN91,
  author = {M. K. Jain and B.-Z. Yu. and J. Rogers and G.N. Ranadive and O.T.
	Berg},
  title = {Interfacial catalysis by phospholipase {A$_2$}: dissociation constants
	for calcium, sunstrate, products and competetive inhibitors},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7306--7317}
}

@ARTICLE{JAME91,
  author = {James, T. L.},
  title = {Relaxation matrix analysis of two-dimensional nuclear overhauser
	effect spectra},
  journal = COSB,
  year = {1991},
  volume = {1},
  pages = {1042--1053}
}

@INCOLLECTION{JENS91,
  author = {E.~V.~Jensen},
  title = {Overview of the Nuclear Receptor Family},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {1--15}
}

@ARTICLE{JONA91,
  author = {R. Jonas and T. G. Ebrey},
  title = {Binding of a Single Divalent Cation Directly Correlates with the
	Blue-to-Purple Transition in Bacteriorhodopsin},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {149--153}
}

@ARTICLE{JONE91,
  author = {A.T. Jones and J.-Y. Zou and S.W. Cowan and M. Kjeldgaard},
  title = {Improved methods for building protein models in electron density
	maps and the location of error in these models},
  journal = ACA,
  year = {1991},
  volume = {47},
  pages = {110--119}
}

@ARTICLE{JUFF91,
  author = {Andr{\'e} H. Juffer and Eugen F. F. Botta and Bert A. M. van Keulen
	and Auke van der Ploeg and Herman J. C. Berendsen},
  title = {The Electric Potential of a Macromolecule in a Solvent: A Fundamental
	Approach},
  journal = JCMP,
  year = {1991},
  volume = {97},
  pages = {144--171},
  number = {1},
  keywords = {continuum electrostatics; solvent; Poisson equation; Poisson-Boltzman
	equation; long range electrostatics; triangulation}
}

@ARTICLE{KALE91,
  author = {L. V. Kal{\'e} and V. Saletore},
  title = {Parallel State-Space Search for a First Solution},
  journal = {Int.\ Journal of Parallel Programming},
  year = {1991},
  volume = {19},
  pages = {251--293},
  publisher = {Plenum Press}
}

@ARTICLE{KATO91,
  author = {Tamaki Kato and Sannamu Lee and Shin Ono and Yukio Agawa and Haruhiko
	Aoyagi and Motonori Ohno and Norikazu Nishino},
  title = {Conformational studies of amphipathic $\alpha$-helical peptides containing
	an amino acid with a long alkyl chain and their anchoring to lipid
	bilayer liposomes},
  journal = BBA,
  year = {1991},
  volume = {1063},
  pages = {191--196}
}

@ARTICLE{KePe91,
  author = {A. D. Kennedy and B. Pendleton},
  title = {Acceptances and Autocorrelations in Hybrid {M}onte {C}arlo},
  journal = {Nuclear Physics B (Proc. Suppl.)},
  year = {1991},
  volume = {20},
  pages = {118--121}
}

@ARTICLE{KERP91,
  author = {T.~K.~Kerppola and T.~Curran},
  title = {Fos-jun heterodimers and jun homodimers bend {\sc DNA} in opposite
	orientations: implications for transcription factor cooperativity.},
  journal = {Cell},
  year = {1991},
  volume = {66},
  pages = {317--326},
  annote = {not read, title tells the rest, it's a eukaryotic transription activator}
}

@ARTICLE{KING91,
  author = {G. King and F.S. Lee and A. Warshel},
  title = {Microscopic simulations of macroscopic dielectric constants of proteins},
  journal = JCP,
  year = {1991},
  volume = {95},
  pages = {4366--4377}
}

@ARTICLE{KiYN91,
  author = {H. Kinoshita and H. Yoshida and H. Nakia},
  title = {Celest.\ Mech.},
  journal = {FIXME},
  year = {1991},
  volume = {50},
  pages = {59--71}
}

@ARTICLE{KIRM91,
  author = {C. Kirmaier and D. Gaul and R. DeBrey and D. Holten and C. Schenk},
  title = {Charge Separation in a Reaction Center Incorporating Bacteriochlorophyll
	for Photoactive Bacteriopheophytin},
  journal = SCI,
  year = {1991},
  volume = {251},
  pages = {922--927}
}

@ARTICLE{KISH91,
  author = {A. Kishigami and N. Sekiya and K. Yoshihara and T. Hara and F. Tokunaga},
  title = {Spectoscopic Studies on the Structures of Retinochrome and Metaretinochrome},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {993--999}
}

@ARTICLE{KLIG91,
  author = {L. H. Kligman},
  title = {The Hairless Mouse and Photoaging},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1109--1118}
}

@ARTICLE{KNOL91,
  author = {W. Knoll and G. Schmidt and H. R{\"o}tzer and T. Henkel and W. Pfeiffer
	and Erich Sackmann and S. Mittler-Neher and J. Spinke},
  title = {Lateral order in binary lipid alloys and its coupling to membrane
	functions},
  journal = CPLI,
  year = {1991},
  volume = {57},
  pages = {363--374},
  annote = {nice introduction},
  keywords = {experimental; membrane; binary mixtures; gramicidin; order-function
	relationship; lipid mixtures; binary phase diagrams; chemically driven
	phase separation; single channel current fluctuations}
}

@ARTICLE{KRAU91,
  author = {P. Kraulis},
  title = {{MOLSCRIPT}---A Program to Produce Both Detailed and Schematic Plots
	of Protein Structures},
  journal = JAC,
  year = {1991},
  volume = {24},
  pages = {946--950}
}

@ARTICLE{Krei91,
  author = {H.-O. Kreiss},
  title = {Problems with different time scales},
  journal = {Acta Numerica},
  year = {1991},
  volume = {1},
  pages = {101--139}
}

@BOOK{KUBY91,
  title = {Enzyme Catalysis, Kinetics, and Substrate Binding},
  publisher = {CRC Press},
  year = {1991},
  author = {Stephen A. Kuby},
  volume = {1},
  series = {Study of enzymes},
  address = {Boca Raton}
}

@ARTICLE{KUND91,
  author = {Craig E. Kundrot and Jay W. Ponder and Frederic M. Richards},
  title = {Algorithms for Calculating Excluded Volume and Its Derivatives as
	a Function of Molecular Conformation and Their Use in Energy Minimization},
  journal = JCC,
  year = {1991},
  volume = {12},
  pages = {402--409},
  number = {3}
}

@ARTICLE{KURI91,
  author = {John Kuriyan and William I. Weis},
  title = {Rigid protein motion as a model for crystallographic temperature
	factors},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {2773--2777}
}

@INCOLLECTION{KURR91A,
  author = {Christian Kurrer and Benno Nieswand and Klaus Schulten},
  title = {Dynamics of Synchronous Neural Activity in the Visual Cortex},
  booktitle = {Artificial Neural Networks},
  publisher = {Elsevier},
  year = {1991},
  editor = {Teuvo Kohonen and Kai M{\"a}kisara and Olli Simula and Jari Kangas},
  pages = {133--138},
  address = {Amsterdam},
  tbtechrep = {TB-91-08}
}

@INCOLLECTION{KURR91B,
  author = {Christian Kurrer and Benno Nieswand and Klaus Schulten},
  title = {A Model for Synchronous Activity in the Visual Cortex},
  booktitle = {Self-Organization, Emergent Properties, and Learning},
  publisher = {Plenum Press},
  year = {1991},
  editor = {A. Babloyantz},
  volume = {260},
  series = NASB,
  pages = {81--95},
  address = {New York}
}

@ARTICLE{KURR91,
  author = {Christian Kurrer and Klaus Schulten},
  title = {Effect of Noise and Perturbations on Limit Cycle Systems},
  journal = PD,
  year = {1991},
  volume = {50},
  pages = {311--320}
}

@INCOLLECTION{KURR91C,
  author = {Christian Kurrer and Klaus Schulten},
  title = {Propagation of Chemical Waves in Discrete Excitable Media: Anisotropic
	and Isotropic Wave Fronts},
  booktitle = {Nonlinear Wave Processes in Excitable Media},
  publisher = {Plenum Press},
  year = {1991},
  editor = {A. V. Holden and M. Markus and H. G. Othmer},
  volume = {244},
  series = NASB,
  pages = {489--500},
  address = {New York}
}

@ARTICLE{LAWR91,
  author = {M.C. Lawrence},
  title = {The Application of the Molecular Replacement Method to the Denovo
	Determination of Protein Structure},
  journal = {Quarterly Reviews of Biophysics},
  year = {1991},
  volume = {24},
  pages = {399--424}
}

@INPROCEEDINGS{LEAT91B,
  author = {Leathrum, Jr., James F. and Board, Jr., John A.},
  title = {Mapping the Adaptive Fast Multipole Algorithm onto MIMD Systems},
  booktitle = {SIAM Proceedings of NASA ICASE workshop on ``Unstructured Parallel
	Scientific Computation''},
  year = {1991},
  publisher = {MIT Press}
}

@INPROCEEDINGS{LEAT91,
  author = {{Leathrum, Jr.}, James F. and {Board, Jr.}, John A.},
  title = {Parallelization of the Fast Multipole Algorithm using the {B012}
	Transputer Network},
  booktitle = {{TRANSPUTING91}},
  year = {1991},
  editor = {Dyke Stiles and Tosiyasu L. Kunii and Andr{\'e} Bakkers},
  volume = {1},
  pages = {296--310}
}

@MISC{LEIG91,
  author = {Leighton, R. and Wieland, A.},
  title = {Aspirin / Migraine Neural Network Package},
  howpublished = {Copyright, The MITRE Corporation, McLean, Va},
  year = {1991}
}

@ARTICLE{LELJ91,
  author = {F. Lelj and P. Grimaldi and P. L. Cristinziano},
  title = {Conformational Energy Minimization by Simulated Annealing Using Molecular
	Dynamics: Some Improvements to the Monitoring Procedure},
  journal = BP,
  year = {1991},
  volume = {31},
  pages = {663--670},
  annote = {Defines constant volume specific heat and fractional fluctuations},
  keywords = {phase transition monitoring}
}

@BOOK{LESK91,
  title = {Protein Architecture},
  publisher = {Oxford University Press},
  year = {1991},
  author = {Arthur M. Lesk},
  address = {New York}
}

@INCOLLECTION{LEVA91,
  author = {S.~LeVay and S.~B. Nelson},
  title = {The columnar organization of visual cortex},
  booktitle = {The Electrophysiology of Vision},
  publisher = {Macmillan Press},
  year = {1991},
  editor = {A.~Leventhal},
  pages = {15--34},
  address = {London}
}

@ARTICLE{LEWI91,
  author = {J. W. Lewis and D. S. Kliger},
  title = {Rotational Diffusion Effects on Absorbance Mesaruments: Limitations
	to the Magic-Angle Approach},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {963--968}
}

@ARTICLE{LIN89,
  author = {Gloria C. Lin and Mostafa A. El-Sayed and Thomas Marti and Lawrence
	J. Stern and Tatushi Mogi and H. Gobind Khorana},
  title = {Effects of individual genetic substitutions of arginine residues
	on the deprotonation and reprotonation kinetics of the {Schiff} base
	during the bacteriorhodopsin photocycle},
  journal = BJ,
  year = {1991},
  volume = {60},
  pages = {172--178},
  number = {1},
  annote = {requested Tx=19921217., clarified Tx=19930201.}
}

@ARTICLE{LIPO91,
  author = {R. Lipowsky},
  title = {The conformation of membranes},
  journal = NAT,
  year = {1991},
  volume = {349},
  pages = {475--481}
}

@TECHREPORT{LOFT91,
  author = {Richard Loft and Klaus Schulten and Andreas Windemuth},
  title = {Slicewise {CM} {FORTRAN} Kernel for the Molecular Dynamics Software
	Package on the {C}onnection {M}achine},
  institution = {University of Illinois},
  year = {1991},
  type = {Beckman Institute Technical Report},
  number = {TB-91-18},
  annote = {Andreas thinks that Loft's first name is Rich, not Richard, but isn't
	sure.},
  tbtechrep = {TB-91-18}
}

@ARTICLE{LOHM91,
  author = {K. J. Lohmann and A. O. D. Willows and R. B. Pinter},
  title = {An Identifiable Molluscan Neuron Responds to Changes in Earth-Strength
	Magnetic Fields},
  journal = {J. Exp. Biol.},
  year = {1991},
  volume = {161},
  pages = {1--24}
}

@ARTICLE{LOOF91,
  author = {Hans de Loof and Stephen C. Harvey and Jere P. Segrest and Richard
	W. Pastor},
  title = {Mean Field Stochastic Boundary Molecular Dynamics Simulation of a
	Phospholipid in a Membrane},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {2099--2113},
  annote = {very long (102ns) simulations of very small systems (7 lipids); tons
	of refs; compares with experimental values; dt=2fs; water penetration;
	many ideas on what to look at},
  keywords = {dipalmitoylphosphatidylcholine DPPC; order parameter}
}

@ARTICLE{SIGL91,
  author = {B.~F.~Luisi and W.~X.~Xu and Z.~Otwinowski and L.~P.~Freedman and
	K.~R.~Yamamoto and P.~B.~Sigler},
  title = {Crystallographic Analysis of the Interaction of the Glucocorticoid
	Receptor with {DNA}},
  journal = NAT,
  year = {1991},
  volume = {352},
  pages = {497--505},
  annote = {this is the article which details the analysis of the GR DBD and
	{DNA} the resolution of the structure is 2.5 , this was originally
	referenced as SIGL92},
  keywords = {GR, DBD,interaction, ligand binding}
}

@ARTICLE{LUND91,
  author = {J. Lund and T. Yoshioka},
  title = {Local Circuit Neurons of Macaque Monkey Striate Cortex: III. Neurons
	of Laminae 4B, 4A, and 3B},
  journal = {J. Comp. Neurol.},
  year = {1991},
  note = {(submitted)}
}

@ARTICLE{LUZH90,
  author = {V. Luzhkov and A. Warshel},
  title = {Microscopic Calculations of Solvent Effects on Absorption Spectra
	of Conjugated Molecules.},
  journal = JACS,
  year = {1991},
  volume = {113},
  pages = {4491--4499}
}

@ARTICLE{MAED91,
  author = {A. Maeda and J. Sasaki and J. Pfefferl{\'e} and Y. Shichida and T.
	Yoshizawa},
  title = {{Fourier} Transform Infrared Spectral Studies on the {Schiff} Base
	Mode of All-{\it trans} Bacteriorhodopsin and its Photointermediates,
	{K} and {L}},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {911--921}
}

@ARTICLE{MARC91,
  author = {Y. L. Marcel and P. R. Prevost and H. Kao and E. Raffai and N. VuDac
	and J.-C. Fruchart and E. Rassart},
  title = {The Epitopes of Apolipoprotein {A-I} Define Distinct Structural Domains
	Including a Mobile Middle Region},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {3644--3653}
}

@ARTICLE{MARK91,
  author = {A. E. Mark and H. J. C. Berendsen and W. F. {van Gunsteren}},
  title = {Conformational Flexibility of Aqueous Monomeric and Dimeric Insulin:
	{A} Molecular Dynamics Study},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {10866--10872}
}

@ARTICLE{MART91F,
  author = {Thomas Marti and Harald Otto and Tasushiu Mogi and Susanne J. R{\"o}sselet
	and Maarten P. Heyn and H. Gobind Khorana},
  title = {Bacteriorhodopsin mutants containing single substitutions of serine
	or threonine residues are all active in proton translocation},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {6919--6927}
}

@ARTICLE{MART91E,
  author = {T. Marti and S. J. R{\"o}sselet and H. Otto and M. P. Heyn and H.
	G. Khorana},
  title = {The Retinylidene {S}chiff Base Counterion in Bacteriorhodopsin},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {18674--18683}
}

@INCOLLECTION{MART91B,
  author = {Thomas Martinetz and Klaus Schulten},
  title = {A ``Neural Gas'' Network Learns Topologies},
  booktitle = {Artificial Neural Networks},
  publisher = {Elsevier},
  year = {1991},
  editor = {Teuvo Kohonen and Kai M{\"a}kisara and Olli Simula and Jari Kangas},
  pages = {397--402},
  address = {Amsterdam},
  tbtechrep = {TB-91-05}
}

@ARTICLE{MARTZ91B,
  author = {E.~Martinez and F.~Givel and W.~Wahli},
  title = {A Common Ancestor {\sc DNA} Motif for Invertebrate and Vertebrate
	Hormone Response Elements},
  journal = EMBO,
  year = {1991},
  volume = {10},
  pages = {263--268},
  annote = {P-box,drosophilia and hsp27 and GR and ERE, more family stuff use
	this to look up XRE sequences}
}

@INCOLLECTION{MART91D,
  author = {E.~Martinez and W.~Wahli},
  title = {Characterization of Hormone Response Elements},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press Limited},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {125--154},
  address = {London, UK, San Diego, CA}
}

@ARTICLE{MATH91,
  author = {R. A. Mathies and S. W. Lin and J. B. Ames and W. T. Pollard},
  title = {From Femtoseconds to Biology: Mechanism of Bacteriorhodopsin's Light-Driven
	Proton Pump},
  journal = ARBB,
  year = {1991},
  volume = {20},
  pages = {491--518}
}

@INPROCEEDINGS{MATT91,
  author = {T. G. Mattson and R. Bjornson and D. Kaminsky},
  title = {Beyond Parallelism to Coordination},
  booktitle = {Proceedings of the Sun Users Group},
  year = {1991},
  address = {San Jose, CA}
}

@ARTICLE{MCCA91,
  author = {J.A. {McCammon}},
  title = {Free energy from simulations},
  journal = {Curr. Opin. Struct. Biol.},
  year = {1991},
  volume = {1},
  pages = {196--200}
}

@ARTICLE{MELC91,
  author = {A. I. Mel\'cuk and R. C. Giles and H. Gould},
  title = {Molecular Dynamics simulation of liquids on the {Connection Machine}},
  journal = CIP,
  year = {1991},
  pages = {311}
}

@ARTICLE{MERE91,
  author = {J. Merenmeies and R. Pihlaskari and J. Laitinen and J. Waritovaara
	and H. Rauvala},
  title = {30-{kDa} heparin-binding protein of brain (amphoterin) involved in
	neurite outgrowth. Amino acid sequence and localization in the filopodia
	of the advancing plasma membrane},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {16722--16729}
}

@INPROCEEDINGS{MICH91a,
  author = {H. Michel},
  title = {General and practical aspects of membrane protein crystallization},
  booktitle = {Crystallization of Membrane Proteins},
  year = {1991},
  editor = {H. Michel},
  pages = {74},
  address = {Boca Raton, Florida},
  publisher = {CRC Press}
}

@ARTICLE{MICH91,
  author = {F. Michelangeli and E. A. Grimes and J. M. East and A. G. Lee},
  title = {Effects of Phospholipids on the Function of {(Ca$^{2+}$--Mg$^{2+}$)-ATPase}},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {342--351},
  annote = {experimental; not on membrane but on enzyme; dioleoylphosphatitylcholine},
  keywords = {ATPase, DOPC}
}

@ARTICLE{MIER91,
  author = {Larry J. W. Mierke and Mary C. Betlach and Alok K. Mitra and Richard
	F. Shand and Susan K. Fong and Robert M. Stroud},
  title = {Wild-type and mutant bacteriorhodopsins {D}85{N}, {D}96{N}, and {R}82{Q}:
	purification to homogeneity, p{H} dependence of pumping, and electron
	diffraction},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {3088--3098}
}

@ARTICLE{MILL91,
  author = {R. H. Miller},
  title = {A Horror Story about Integration Methods},
  journal = JCMP,
  year = {1991},
  volume = {93},
  pages = {469--476},
  annote = {compares leap frog algorithm with predictor-corrector algorithm;
	leap frog is better; being symplectic seems to be essential},
  keywords = {Verlet; symplectic; Chirikov map}
}

@ARTICLE{MITC91,
  author = {Drake C. Mitchell and Julia Kibelbek and Burton J. Litman},
  title = {Rhodopsin in Dimyristoylphosphatidylcholine-Reconstituted Bilayers
	Forms Metarhodopsin~{II} and Activates G$_{\rm t}$},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {37--42},
  annote = {get to liquid-crystal transition of membrane influences activity
	of rhodopsin; activity of rhodopsin is much higher in the liquid
	crystal pahse, but in both still less than in the natural disk membrane;
	phase transition for DMPC at 23C...24C},
  keywords = {G-protein; rhodopsin; DMPC; POPC}
}

@ARTICLE{MOND91,
  author = {A.~Mondragon and S.~C.~Harrison},
  title = {The Phage 434 {CRO--OR1} complex at {2.5\,\AA} resolution},
  journal = {J.\ Mol.\ Biol.},
  year = {1991},
  volume = {219},
  pages = {321--334},
  annote = {DNA bends around protein, a.axis symmetry not same for pro and DNA
	b.dimer interactions not symmetric c.intersting stuff in discussion.
	genral pro-dna and pro-pro stuff for a similar system d.discusses
	non-watson crick base-pair interactions (base-pairing out of hte
	plane, is accompanied by increased twist, check this) e.should actually
	get struct from PDB and check it out}
}

@ARTICLE{MOUN91,
  author = {Raymond D. Mountain and D. Thirumalai},
  title = {Ergodic measures for the simulation of dielectric properties of water},
  journal = CPC,
  year = {1991},
  volume = {62},
  pages = {352--359},
  annote = {need 500ps...1000ps to equilibrate water @ 300K; diffusion constant
	of water $D_\mu = 0.16 ps^{-1}$ @ 313K [the unit is not complete,
	obscure article] (varies strongly with temperature},
  keywords = {SPC water}
}

@ARTICLE{MUGA91,
  author = {A. Muga and H.H. Mantsch and W.K. Surewicz},
  title = {Membrane writing induces destabilization of {C}ytochrome C structure},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {7219--7224},
  annote = {{FTIR} studies of peripheral membrane proteins}
}

@ARTICLE{MUKO91,
  author = {Y. Mukohata and K. Ihara and K. Uegaki, Y. Miyashita and Y. Sugiyama},
  title = {Australian {\it Halobacteria} and their Retinal-{Protein} Ion Pumps},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1039--1045}
}

@INCOLLECTION{MULL91,
  author = {M.~Muller and C.~Baniahmad and C.~Kaltschmidt and R.~Sch{\"u}le and
	R.~Renkawitz},
  title = {Co-operative Transactivation of Steroid Receptors},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {155--174}
}

@ARTICLE{MURD91,
  author = {F.~Murdoch and K.~A.~A.~Grunwald and J.~Gorski},
  title = {Marked Effects of Salt on Estrogen Receptor Binding to {DNA}: Biologically
	Relevant Discrimination between {DNA} Sequences},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {10838--10844},
  annote = {approximately 4 ions are released upon ER binding DNA}
}

@TECHREPORT{NABO91,
  author = {K. Nabors and J. White},
  title = {FastCap: A Multipole Accelerated 3-D Capacitance Extraction Program},
  institution = {MIT Dept. of Electrical Engineering and Computer Science Preprint},
  year = {1991}
}

@ARTICLE{NAGL91,
  author = {J. F. Nagle},
  title = {Photocycle Kinetics: Analysis of Raman Data From Bacteriorhodopsin},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {897--903}
}

@ARTICLE{NASR91,
  author = {N. Nasrin and C. Buggs and X. F. Kong and J. Carnazza and M. Goebl
	and M. Alexander-Bridges},
  title = {{DNA}-binding properties of the product of the testis-determining
	gene and a related protein},
  journal = NAT,
  year = {1991},
  volume = {354},
  pages = {317--320}
}

@ARTICLE{NEED91,
  author = {Needleman, R. and Chang, M. and Ni, B. and Varo, G. and Fornes, J.
	and White, Stephen H. and Lanyi, J. K.},
  title = {Properties of {Asp}$^{212}$ $\rightarrow$ {Asn} Bacteriorhodopsin
	Suggest That {Asp}$^{212}$ and {Asp}$^{85}$ Both Participate in a
	Counterion and Proton Complex near the {Schiff} Base},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {11478--11484}
}

@ARTICLE{NEWT91,
  author = {M. D. Newton},
  title = {Quantum Chemical Probes of Electron-Transfer Kinetics: The Nature
	of Donor-Acceptor Interactions},
  journal = CR,
  year = {1991},
  volume = {91},
  pages = {767--792}
}

@ARTICLE{NICH91,
  author = {A. Nicholls and K. A. Sharp and B. Honig},
  title = {Protein Folding and Association: Insights From the Interfacial and
	Thermodynamic Properties of Hydrocarbons},
  journal = {Proteins: Structure, Function and Genetics},
  year = {1991},
  volume = {11},
  pages = {281--296},
  number = {4},
  annote = {reference for GRASP}
}

@ARTICLE{NILG91a,
  author = {M. Nilges and A. Br{\"u}nger},
  title = {Automated Modeling of Coiled Coils: Application to the {GCN4} dimerization
	region},
  journal = {Protein Engineering},
  year = {1991},
  volume = {4},
  pages = {649--659},
  number = {6}
}

@ARTICLE{NILG91,
  author = {M. Nilges and J. Habazettl and A. T. Br{\"u}nger and T. A. Holak},
  title = {Relaxation Matrix Refinement of the Solution Structure of Squash
	Trypsin-Inhibitor},
  journal = {J. Mol. Biol.},
  year = {1991},
  volume = {219},
  pages = {499--510}
}

@ARTICLE{NONE91,
  author = {Marco Nonella and Klaus Schulten},
  title = {Molecular Dynamics Simulation of Electron Transfer in Proteins: {T}heory
	and Application to {Q$_A$ $\rightarrow$ Q$_B$} Transfer in the Photosynthetic
	Reaction Center},
  journal = JPC,
  year = {1991},
  volume = {95},
  pages = {2059--2067}
}

@ARTICLE{NONE91A,
  author = {Marco Nonella and Andreas Windemuth and Klaus Schulten},
  title = {Structure of Bacteriorhodopsin and {\em in situ} Isomerization of
	Retinal: A Molecular Dynamics Study},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {937--948},
  number = {6},
  tbtechrep = {TB-91-03}
}

@INCOLLECTION{ObBS91,
  author = {Klaus Obermayer and Gary G. Blasdel and Klaus Schulten},
  title = {A Neural Network Model for the Formation and for the Spatial Structure
	of Retinotopic Maps, Orientation- and Ocular Dominance Columns},
  booktitle = {Artificial Neural Networks},
  publisher = {Elsevier},
  year = {1991},
  editor = {Teuvo Kohonen and Kai M{\"a}kisara and Olli Simula and Jari Kangas},
  pages = {505--511},
  address = {Amsterdam},
  tbtechrep = {TB-91-09}
}

@INCOLLECTION{OBER91A,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {Development and Spatial Structure of Cortical Feature Maps: A Model
	Study},
  booktitle = {Advances in Neural Information Processing Systems~3},
  publisher = {Morgan Kaufmann},
  year = {1991},
  editor = {D. Touretzky and R. Lippman},
  pages = {11--17},
  address = {San Mateo CA}
}

@ARTICLE{OEST91,
  author = {D. Oesterhelt and C. Brauchle and N. Hampp},
  title = {Bacteriorhodopsin\ --\ A Biological-Material for Information-Processing},
  journal = QRB,
  year = {1991},
  volume = {24},
  pages = {425--478}
}

@ARTICLE{OOI91,
  author = {Ooi, T. and Oobataki, M.},
  title = {Prediction of the Thermodynamics of Protein Folding: The helix-Coil
	Transition of Poly({L}-alanine)},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {2859--2863}
}

@ARTICLE{Oteo91,
  author = {J. A. Oteo},
  title = {The {B}aker-{C}ampbell-{H}ausdorff formula and nested commutator
	identities},
  journal = JMP,
  year = {1991},
  volume = {32},
  pages = {419--424}
}

@ARTICLE{OTTO91,
  author = {H. Otto and M. P. Heyn},
  title = {Between the Ground- and M-State of Bacteriorhodopsin the Retinal
	Transition Dipole Moment Tilts Out of the Plane of the Membrane by
	Only 3$^\circ$},
  journal = FEBS,
  year = {1991},
  volume = {293},
  pages = {111--114}
}

@ARTICLE{PARI91,
  author = {M. A. Parisi and D. A. Clayton},
  title = {Similarity of human mitochondrial transcription factor 1 to to high
	mobility group proteins},
  journal = SCI,
  year = {1991},
  volume = {255},
  pages = {965--969}
}

@ARTICLE{PASC91,
  author = {J.-L. Pascal-Ahuir and E. L. Mehler and H. Weinstein},
  title = {Calmodulin Structure and Function: Implication of Arginine in the
	Compaction Related to Ligand Binding},
  journal = MENG,
  year = {1991},
  volume = {1},
  pages = {231--247}
}

@ARTICLE{PAST91,
  author = {Richard W. Pastor and Richard M. Venable and Martin Karplus},
  title = {Model for the Structure of the Lipid Bilayer},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {892--896},
  annote = {mean field; single chain simulation; 84 lipid-assembly; trans-gauche
	isomerization rates; important experimental data one has to reproduce:
	order parameters, C13 T1 relaxation times, surface area/head group
	68.1--71AA^2, diffusion constants, isomerization rates, average chain
	length, volume per methylene group (density); $\gamma$=50 ps^-1;
	gives simulation parameters; idea for color pictures; has thickness
	data},
  keywords = {$^2$H order parameters; chain-tilt Marcelja model; computer simulations;
	membrane; Brownian dynamics; cone model; DPPC}
}

@ARTICLE{PeTW91,
  author = {Jeffery W. Peng and V. Thanabal and Gerhard Wagner},
  title = {{2D} Heteronuclear {NMR} Measurements of {S}pin-{L}attice Relaxation
	Times in the Rotating Frame of {X} Nuclei in Heteronuclear {HX} Spin
	Systems},
  journal = JMR,
  year = {1991},
  volume = {94},
  pages = {82--100}
}

@ARTICLE{PEPP91,
  author = {D. Pepperberg and T. Okajima and H. Pipps and G. Chader and B. Wiggert},
  title = {Functional Propeties of Interphotoreceptor Retinoid-binding Protein},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1057--1060}
}

@ARTICLE{PFEF91,
  author = {J. Pfefferl{\'e} and A. Maeda and J. Sasaki and T. Yoshizawa},
  title = {{Fourier} Transform Infrared Study of the {N} Intermediate of Bacteriorhodopsin},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {6548--6556}
}

@ARTICLE{PUET91,
  author = {Benno P{\"u}tz and Daniel Barsky and Klaus Schulten},
  title = {Edge Enhancement by Diffusion: Microscopic Magnetic Resonance Imaging
	of an Ultra-Thin Glass Capillary},
  journal = CPL,
  year = {1991},
  volume = {183},
  pages = {391--396},
  number = {5},
  tbtechrep = {TB-91-02}
}

@CONFERENCE{PUET91D,
  author = {Benno P{\"u}tz and Daniel Barsky and Klaus Schulten},
  title = {Edge Enhancement in Microscopic MRI},
  booktitle = {Tenth Annual Scientific Meeting and Exhibition, Works in Progress},
  year = {1991},
  pages = {1252},
  publisher = {Society of Magnetic Resonance in Medicine, Inc.}
}

@ARTICLE{QiWZ91,
  author = {M.-Z. Qin and D.-L. Wang and M.-Q. Zhang},
  title = {Explicit Symplectic Difference Schemes for Separable {H}amiltonian
	Systems},
  journal = {J. Comput.\ Math.},
  year = {1991},
  volume = {9},
  pages = {211--221},
  number = {3}
}

@UNPUBLISHED{QiZh91,
  author = {M.-Z. Qin and W.-J. Zhu},
  title = {Canonical \mbox{Runge-Kutta-Nystr\"om(RKN)} Methods for Second Order
	Ordinary Differential Equations},
  note = {Preprint},
  year = {1991}
}

@ARTICLE{RAMI91,
  author = {F. Ramirez and M. K. Jain},
  title = {Phospholipase~{A}$_2$ at the Bilayer Interface},
  journal = PSFG,
  year = {1991},
  volume = {9},
  pages = {229--239}
}

@ARTICLE{RAUS91,
  author = {J.~Rauschecker},
  title = {Mechanisms of visual plasticity: Hebb synapses, {NMDA} receptors,
	and beyond},
  journal = {Physiol. Rev.},
  year = {1991},
  volume = {71},
  pages = {587--615}
}

@ARTICLE{REME91,
  author = {D. P. Remeta and C. P. Mudd and R. L. Berger and K. J. Breslauer},
  title = {Thermodynamic Characterization of Daunomycin-{DNA} Interactions:
	Microcalorimetric Measurements of Daunomycin-{DNA} Binding Enthalpies},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {9799--9809}
}

@INCOLLECTION{RITT91,
  author = {Helge Ritter and Klaus Obermayer and Klaus Schulten and Jeanne Rubner},
  title = {Self-Organizing Maps and Adaptive Filters},
  booktitle = {Models of Neural Networks},
  publisher = {Springer--Verlag},
  year = {1991},
  editor = {J. Leo van Hemmen and Eytan Domany and Klaus Schulten},
  series = {Physics of Neural Networks},
  pages = {281--306},
  address = {New York},
  annote = {Probably this book is volume 1 in the series, but this fact is not
	mentioned on the title page.}
}

@ARTICLE{ROBE91,
  author = {Miranda Robertson},
  title = {Membrane proteins and minimalism},
  journal = NAT,
  year = {1991},
  volume = {354},
  pages = {183},
  annote = {editorial}
}

@ARTICLE{RODR91,
  author = {Rodriguez, G. and Jain, A. and Kreutz, K.},
  title = {A Spatial Operator Algebra for Manipulator Modeling and Control},
  journal = {The International Journal of Robotics Research},
  year = {1991},
  volume = {10},
  pages = {371--381}
}

@ARTICLE{ROIT91,
  author = {A. Roitberg and R. Elber},
  title = {Modelling side chains in peptides and proteins: Application of the
	locally enhanced sampling technique and the simulated annealing methods
	to find minimum energy conformations},
  journal = {J. Chem. Phys},
  year = {1991},
  volume = {95},
  pages = {9277--9287}
}

@ARTICLE{ROTH91,
  author = {S. M. Roth and D. M. Schneider and L. A. Strobel and M. F. A. VanBerkum
	and A. R. Means and A. J. Wand},
  title = {Structure of the Smooth Muscle Myosin Light Chain Kinase Calmodulin
	Binding Domain Bound to Calmodulin},
  journal = {Biochemistry},
  year = {1991},
  volume = {30},
  pages = {10078--10084}
}

@ARTICLE{ROUX91,
  author = {Roux, B. and Karplus, M.},
  title = {Ion transport in a model gramicidin model - structure and thermodynamics},
  journal = BCH,
  year = {1991},
  volume = BJ,
  pages = {961--981}
}

@ARTICLE{Rowl91,
  author = {G. Rowlands},
  title = {A Numerical Algorithm for {H}amiltonian Systems},
  journal = {J. Comput.\ Phys.},
  year = {1991},
  volume = {97},
  pages = {235--239},
  nremark = {Rowlands' method---motivated as in the analysis of MTS methods paper}
}

@ARTICLE{SAIT91,
  author = {Hiroshi Saito and Tsunehisa Araiso and Haruisa Shirahama and Tomiyasu
	Koyama},
  title = {Dynamics of the Bilayer-Water Interface of Phospholipid Vesicles
	and the Effect of Cholesterol: A Picosecond Fluorescence Anisotropy
	Study},
  journal = JB,
  year = {1991},
  volume = {109},
  pages = {559--565}
}

@ARTICLE{SAMP91,
  author = {Prakash Sampath and Thomas D. Pollard},
  title = {Effects of Cytochalasin, Phalloidin, and {pH} on the Elongation of
	Actin Filaments},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {1973--1980}
}

@ARTICLE{SANT91,
  author = {R. Santus},
  title = {The Photobiology of the Living Cell as Studied by Microspectrofluorometric
	Techniques},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1071--1077}
}

@INCOLLECTION{Sanz91,
  author = {J. M. Sanz-Serna},
  title = {Two Topics in Nonlinear Stability},
  booktitle = {Advances in Numerical Analysis},
  publisher = {Clarendon Press},
  year = {1991},
  editor = {Will Light},
  pages = {147--174},
  address = {Oxford}
}

@ARTICLE{SaAb91,
  author = {J. M. Sanz-Serna and L. Abia},
  title = {Order conditions for canonical \mbox{Runge-Kutta} schemes},
  journal = SJNA,
  year = {1991},
  volume = {28},
  pages = {1086--1091}
}

@ARTICLE{SCHE91a,
  author = {S. Scheiner and X. Duan},
  title = {Effect of intermolecular orientation upon proton transfer within
	a polarizable medium},
  journal = BJ,
  year = {1991},
  volume = {60},
  pages = {874--883}
}

@ARTICLE{SCHE91,
  author = {G. F. X. Schertler and R. Lozier and H. Michel and D. Oesterhelt},
  title = {Chromophore Motion During the Bacteriorhodopsin Photocycle: Polarized
	Absorption Spectroscopy of Bacteriorhodopsin and its M-State in Bacteriorhodopsin
	Crystals},
  journal = EMBO,
  year = {1991},
  volume = {10},
  pages = {2353--2361}
}

@ARTICLE{SCHI91A,
  author = {J. L. Schiano and R. L. Magin and A. G. Webb and S. M. Wright},
  title = {Feedback control of the nuclear magnetization state},
  journal = {Proceedings of the 32nd Experimental Nuclear Magnetic Resonance Conference},
  year = {1991},
  address = {St. Louis, MO}
}

@ARTICLE{SCHI91B,
  author = {J. L. Schiano and R. L. Magin and S. M. Wright},
  title = {Feedback control of the nuclear magnetization state: modeling and
	control design},
  journal = {IEEE Trans. Med. Imaging (MI-10, no. 2)},
  year = {1991}
}

@ARTICLE{SCHI91C,
  author = {J. L. Schiano and A. G. Webb and R. L. Magin},
  title = {Flip angle optimization in fast MRI using adaptive feedback control},
  journal = {Proceedings of the 1991 Society of Magnetic Resonance in Medicine},
  year = {1991},
  address = {San Francisco, CA}
}

@ARTICLE{SCHM91,
  author = {K. E. Schmidt and M. A. Lee},
  title = {Implementing the Fast Multipole Method in Three Dimensions},
  journal = JSP,
  year = {1991},
  volume = {63},
  pages = {1223--1235}
}

@ARTICLE{ScLe91,
  author = {K. E. Schmidt and M. A. Lee},
  title = {Implementing the fast multipole method in three dimensions},
  journal = {J. Stat.\ Phys.},
  year = {1991},
  volume = {63},
  pages = {1223--1235}
}

@ARTICLE{SCHN91,
  author = {T. D. Schneider},
  title = {Theory of Molecular Machines. {II. Energy} Dissipation from Molecular
	Machines},
  journal = JTB,
  year = {1991},
  volume = {148},
  pages = {125--137},
  number = {1}
}

@ARTICLE{SCHO91,
  author = {Scholtz, J. M. and Marqusee, S. and Baldwin, R. L. and York, E. J.
	and Stewart, J. M. and Santoro, M. and Bolen, D. W.},
  title = {Calorimetric Determination of the Enthalpy Change for the $\alpha$-Helix
	to Coil Transition of an Alanine Peptide in Water},
  journal = PNAS,
  year = {91},
  volume = {88},
  pages = {2854--2858}
}

@ARTICLE{SCHU91A,
  author = {Klaus Schulten and Markus Tesch},
  title = {Coupling of Protein Motion to Electron Transfer: Molecular Dynamics
	and Stochastic Quantum Mechanics Study of Photosynthetic Reaction
	Centers},
  journal = CP,
  year = {1991},
  volume = {158},
  pages = {421--446},
  tbtechrep = {TB-91-15}
}

@ARTICLE{TESC91,
  author = {Klaus Schulten and Markus Tesch},
  title = {Coupling of Protein Motion to Electron Transfer: Molecular Dynamics
	and Stochastic Quantum Mechanics Study of Photosynthetic Reaction
	Centers},
  journal = CP,
  year = {1991},
  volume = {158},
  pages = {421--446},
  tbtechrep = {TB-91-15}
}

@ARTICLE{SCHL91,
  author = {S. C. Schultz and G. C. Schields and T. A. Steitz},
  title = {Crystal structure of a {CAP-DNA} complex: {The DNA} is bent by $90^\circ$},
  journal = SCI,
  year = {1991},
  volume = {253},
  pages = {1001}
}

@ARTICLE{SCHU91B,
  author = {S. C. Schultz and G. C. Schields and T. A. Steitz},
  title = {Crystal structure of a {CAP-DNA} complex: {The DNA} is bent by $90^\circ$},
  journal = SCI,
  year = {1991},
  volume = {253},
  pages = {1001--1007}
}

@ARTICLE{SCHW91B,
  author = {J.~W.~R.~Schwabe and D.~Rhodes},
  title = {Beyond zinc fingers: steroid hormone receptors have a novel structural
	motif for {DNA} recognition},
  journal = TIBS,
  year = {1991},
  volume = {16},
  pages = {291--296},
  annote = {solution structure of ER and GR DBD's cite also Schwabe90 and Hard
	90}
}

@ARTICLE{SCHW91,
  author = {Robert Schwyzer},
  title = {Peptide-Membrane Interactions and a New Priciple in Quantitative
	Structure-Activity Relationships},
  journal = BP,
  year = {1991},
  volume = {31},
  pages = {785--792},
  annote = {Importance of membrane for structure-function relationship; overview;
	many refs},
  keywords = {gramizidin}
}

@ARTICLE{SCOT91,
  author = {D. L. Scott and S. P. White and J. L. Browning and J. J. Rosa and
	M. H. Gelb and P. B. Sigler},
  title = {Structures of Free and Inhibited Human Secretory Phospholipase {A}$_2$
	from Inflammatory Exudate},
  journal = SCI,
  year = {1991},
  volume = {254},
  pages = {1007--1010}
}

@INPROCEEDINGS{Scov91a,
  author = {C. Scovel},
  title = {Symplectic Numerical Integration of \mbox{Hamiltonian} Systems},
  booktitle = {The Geometry of {H}amiltonian Systems: Proceedings of Workshop Held
	June 5--16, 1989},
  year = {1991},
  editor = {T.~Ratiu},
  pages = {463--496},
  organization = {Mathematical Sciences Research Institute, Springer-Verlag}
}

@ARTICLE{Scov91b,
  author = {Clint Scovel},
  title = {On symplectic lattice maps},
  journal = {Physics Letters A},
  year = {1991},
  volume = {159},
  pages = {396--400}
}

@INPROCEEDINGS{SEMM91,
  author = {P. Semm and T. Schneider},
  title = {Magnetic responses in the central nervous system of birds},
  booktitle = {Effects of atmospherical and geophysical variables in biology and
	medicine},
  year = {1991},
  editor = {H. Lieth},
  pages = {3--13},
  publisher = {Progr.\ Biometerol.\ 8}
}

@ARTICLE{SEN91,
  author = {Arindam Sen and Thomas V.\ Isac and Sek--Wen Hui},
  title = {Bilayer Packing Stress and Defects in Mixed Dilinoleoylphosphatidylethanolamine
	and Palmitoyloleoylphosphatidylcholine and Their Susceptibility to
	Phospholipase {A$_2$}},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {4516--4521}
}

@ARTICLE{SHAR91A,
  author = {A. Y. Sharonov and N. V. Tkachenko and V. V. Savransky and A. K.
	Dioumaev},
  title = {Time-Resolved Ultraviolet Absorption Changes in the Photocycle of
	Bacteriorhodopsin},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {889--895}
}

@ARTICLE{SHAR91,
  author = {Kim A. Sharp and Anthony Nicholls and Richard F. Fine and Barry Honig},
  title = {Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic
	Effects},
  journal = SCI,
  year = {1991},
  volume = {252},
  pages = {106--109}
}

@ARTICLE{SHKR91,
  author = {I. A. Shkrob and V. F. Tarasov and A. L. Buchachenko},
  title = {Electron spin exchange in micellized radical pairs. II. Magnetic
	field and magnetic isotope effects in multinuclear pairs},
  journal = {Chemical Physics},
  year = {1991},
  volume = {153},
  pages = {443--456},
  number = {3}
}

@ARTICLE{SHRE91,
  author = {A. P. Shreve and J. K. Trautman and H. A. Frank and T. G. Owens and
	A. C. Albrecht},
  title = {Femtosecond Energy-transfer Processes in the B800-850 Light-harvesting
	Complex of {\em Rhodobacter sphaeroides}-2.4.1},
  journal = BBA,
  year = {1991},
  volume = {1058},
  pages = {280--288}
}

@ARTICLE{SHRE91A,
  author = {A. P. Shreve and J. K. Trautman and T. G. Owens and A. C. Albrecht},
  title = {Determination of the {S}$_2$ lifetime of $\beta$ carotene},
  journal = CPL,
  year = {1991},
  volume = {178},
  pages = {89--96}
}

@ARTICLE{SIMO91,
  author = {Thomas Simonson and David Perahia and G{\'e}rard Bricogne},
  title = {Intramolecular Dielectric Screening in Proteins},
  journal = JMB,
  year = {1991},
  volume = {218},
  pages = {859--886}
}

@ARTICLE{Skee91,
  author = {R.~D. Skeel},
  title = {Macromolecular Dynamics on a Shared-Memory Multiprocessor},
  journal = JCC,
  year = {1991},
  volume = {12},
  pages = {175--179},
  number = {2},
  annote = {I changed this one FROM SKEE89 to SKEE91, as 1991 is the real year
	it was published. HH, also, Rpt. No. 929, Center for Supercomputing
	Research and Development, Univ. of Illinois, Urbana, 1989}
}

@ARTICLE{SMIT91,
  author = {M. Mitchell Smith},
  title = {Histone structure and function},
  journal = COCB,
  year = {1991},
  volume = {3},
  pages = {429--437}
}

@INPROCEEDINGS{SNED91,
  author = {D.~J. Sneddon and C. L. {Brooks~{III}}},
  title = {Molecular Structures in Biology},
  year = {1991},
  editor = {K. Prout},
  address = {Oxford},
  publisher = {Oxford University Press},
  note = {In press}
}

@BOOK{Sobc91,
  title = {Stochastic Differential Equations},
  publisher = {Kluwer},
  year = {1991},
  author = {K. Sobczyk},
  place = {Dordrecht}
}

@ARTICLE{SOK91,
  author = {R. M. Sok and J. C. Berendsen and W. F. van Gunsteren},
  title = {Molecular dynamics simulation of the transport of small molecules
	across a polymer membrane},
  journal = JCP,
  year = {1991},
  volume = {96},
  pages = {4699--4704},
  annote = {Diffusion constant and partition coefficient calculated for He and
	Methane in polydimethylsiloxane. Particle insertion method, monitoring
	of void volumes in dynamical membrane.}
}

@ARTICLE{SPER91a,
  author = {M.M. Sperotto and O.G. Mouritsen},
  title = {Mean-field and {M}onte {C}arlo simulation studies of the lateral
	distribution of proteins in membranes},
  journal = {Eur Biophys J},
  year = {1991},
  volume = {19},
  pages = {157--168}
}

@ARTICLE{SPER91b,
  author = {M.M. Sperotto and O.G. Mouritsen},
  title = {{M}onte {C}arlo simulation studies of lipid order parameter profiles
	near integral membrane proteins},
  journal = BJ,
  year = {1991},
  volume = {59},
  pages = {261--270}
}

@ARTICLE{SPIK91,
  author = {J. D. Spikes},
  title = {Applications of Dye-{Sensitized} Photoreactions in Neurobiology},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1079--1092}
}

@ARTICLE{STEI91,
  author = {G. Steinberg and N. Friedman and M. Sheves and M. Ottolenghi},
  title = {Isomer compostion and spectra of the dark and light adapted forms
	of artifical bacteriorhodopsins},
  journal = PCPB,
  year = {1991},
  volume = {54},
  pages = {969--676}
}

@ARTICLE{STIG91,
  author = {Dirk Stigter and Darwin O. V. Alonso and Ken A. Dill},
  title = {Protein stability: Electrostatics and compact denaturated states},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {4176--4180},
  keywords = {molten globule; statistical mechanics; protein folding; heteropolymers;
	free energy; smeared charges}
}

@ARTICLE{SUBR91A,
  author = {Sriram Subramaniam and Duncan A. Greenhalgh and Parshuram Rath and
	Kenneth J. Rotshild and H. Gobind Khorana},
  title = {Replacement of Leucine-93 by Alanine or Threonine Slows Down the
	Decay of the N and O Intermediates in the Photocycle of Bacteriorhodopsin:
	{I}mplications for Proton Uptake and 13-{\it cis}-Retinal $\rightarrow$
	all-{\it trans}-Retinal Reisomerisation},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {6873--6877}
}

@ARTICLE{SUBR91,
  author = {S. Subramaniam and T. Marti adn S. J. R{\"o}sselet and K. J. Rothschild
	and H. G. Khorana},
  title = {The Reaction of Hydroxylamine with Bacteriorhodopsin Studied With
	Mutants That Have Altered Photocycles: Selective Reactivity of Different
	Photointermediates},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {2583--2587}
}

@INCOLLECTION{SUND91,
  author = {V. Sundstrom and R. {van Grondelle}},
  title = {Dynamics of excitation energy transfer in photosynthetic bacteria},
  booktitle = {Chlorophylls},
  publisher = {CRC Press},
  year = {1991},
  editor = {H. Scheer},
  pages = {627--704},
  address = {Boca Raton}
}

@ARTICLE{Suzu91,
  author = {Masuo Suzuki},
  title = {General Theory of Fractal Path Integrals with Applications to Many-body
	Theories and Statistical Physics},
  journal = {J. Math.\ Phys.},
  year = {1991},
  volume = {32},
  number = {2},
  nremark = {explicit SIs of order > 2 have at least one negative weight}
}

@ARTICLE{SWAM91,
  author = {S. Swaminathan and G. Ravishanker and D. L. Beveridge},
  title = {Molecular Dynamics of {B-DNA} Including Water and Counterions: A
	140 ps Trajectory for d({CGCGAATTCGCG}) Based on the {GROMOS} Force
	Field},
  journal = JACS,
  year = {1991},
  volume = {113},
  pages = {5027--5040},
  annote = {see it for refs to other simulations, hydration, watson-crick base-pairing
	function to maintain stability, 140ps simulaiton of B-DNA, i don't
	really think that the paper is written well, but can ref it for information
	on dials and windows,location of counterions along OPO bisector}
}

@ARTICLE{SZUT91,
  author = {Ete Z. Szuts and Ferenc I. Harosi},
  title = {Solubility of Retinoids in Water},
  journal = {Archives of Biochemistry and Biophysics},
  year = {1991},
  volume = {287},
  pages = {297--304}
}

@ARTICLE{TAM91,
  author = {C. M. Tam and T. Matsuura and A. Y. Tremblay},
  title = {The Fractal Nature of Membranes},
  journal = JCIS,
  year = {1991},
  volume = {147},
  pages = {206--212},
  number = {1},
  keywords = {synthetical membranes; pores}
}

@ARTICLE{TEET91,
  author = {M. M. Teeter},
  title = {Water-protein interactions: {Theory} and experiment},
  journal = ARBBC,
  year = {1991},
  volume = {20},
  pages = {577--600}
}

@ARTICLE{THOM91,
  author = {M. Thompson and M. Zerner},
  title = {A Theoretical Examination of the Electronic Structure and Spectroscopy
	of the Photosynthetic Reaction Center from {\it Rhodopseudomanas
	viridus}},
  journal = JACS,
  year = {1991},
  volume = {113},
  pages = {8210--8215}
}

@ARTICLE{THUR91,
  author = {H. Thurnhofer and J. Schnabel and M. Betz and G. Lipka and C. Pidgeon
	and H. Hauser},
  title = {Cholesterol transfer protein located in the intestinal brush-border
	membrane partial purification and characterization},
  journal = BBA,
  year = {1991},
  volume = {1064},
  pages = {275--286}
}

@ARTICLE{TOBI90,
  author = {D.~J. Tobias and Charles L. {Brooks~{III}}},
  title = {The Thermodynamics and Mechanism of Alpha Helix Initiation in Alanine
	and Valine Peptides},
  journal = {Biochemistry},
  year = {1991},
  note = {In press}
}

@ARTICLE{TONG91,
  author = {L. A. Tong and A. M. {de\,Vos} and M. V. Milburn and S. H. Kim},
  title = {Crystal structure at 2.2\,{{\AA}} resolution of the catalytic domains
	of normal ras protein and an oncogenic mutant complexed with {GDP}},
  journal = JMB,
  year = {1991},
  volume = {217},
  pages = {503--516}
}

@ARTICLE{TORD91,
  author = {Andrew E. Torda and Wilfried F. van Gunsteren},
  title = {The refinement of {NMR} structures by molecular dynamics simulation},
  journal = CPC,
  year = {1991},
  volume = {62},
  pages = {289--296},
  annote = {a very interesting paper, well written; shows many open questions},
  keywords = {NOE; J-coupling}
}

@ARTICLE{TRAV91,
  author = {A. A. Travers},
  title = {{DNA} bending and kinking},
  journal = {Curr. Opin. Struct. Biol.},
  year = {1991},
  volume = {1},
  pages = {114--122}
}

@ARTICLE{TRET91,
  author = {A. Tretyn and R. Kendrick and G. Wagner},
  title = {The Role of Calcium Ions in Phytochrome Action},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1135--1155}
}

@INCOLLECTION{TrCo91,
  author = {J. M. Troyer and F. E. Cohen},
  title = {Simplified Models for Understanding and Predicting Protein Structure},
  booktitle = {Reviews in Computational Chemistry II},
  publisher = {VCH Publishers},
  year = {1991},
  editor = {K. B. Lipkowitz and D. B. Boyd},
  pages = {57--80},
  address = {New York}
}

@INCOLLECTION{TSAI91,
  author = {S.~Y.~Tsai and M.~-J.~Tsai and B.~W.~O'Malley},
  title = {The Steroid Receptor Superfamily: Transactivators of Gene Expression},
  booktitle = {Nuclear Hormone Receptors},
  publisher = {Academic Press},
  year = {1991},
  editor = {M.~G.~Parker},
  pages = {103--124}
}

@ARTICLE{TuBe91a,
  author = {M.E. Tuckerman and B.J. Berne},
  title = {Molecular dynamics algorithm for multiple time scales: systems with
	long range forces},
  journal = JCP,
  year = {1991},
  volume = {94},
  pages = {6811--6815},
  number = {10}
}

@ARTICLE{TuBe91b,
  author = {Mark E. Tuckerman and Bruce J. Berne},
  title = {Molecular Dynamics in Systems with Multiple Time Scales: Systems
	with Stiff and Soft Degrees of Freedom and with Short and Long Range
	Forces},
  journal = JCP,
  year = {1991},
  volume = {95},
  pages = {8362--8364},
  number = {11},
  nremark = {CALL NO: 530.5JOUC}
}

@ARTICLE{UMES91,
  author = {K.~Umesono and K.~K.~Murakami and C.~C.~Thompson and R.~M.~Evans},
  title = {Direct repeats as selective response elements for the thyroid hormone,
	retinoic acid and vitamin {D}${_3}$ receptors.},
  journal = CEL,
  year = {1991},
  volume = {65},
  pages = {1255--1266}
}

@ARTICLE{VARO91A,
  author = {G. V\'{a}r\'{o} and J. K. Lanyi},
  title = {Thermodynamics and Energy Coupling in the Bacteriorhodopsin Photocycle},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {5016--5022}
}

@ARTICLE{VARO91B,
  author = {G. V\'{a}r\'{o} and J. K. Lanyi},
  title = {Kinetic and Spectroscopic Evidence for an Irreversible Step Between
	Deprotonation and Reprotonation of the {Schiff}-Base in the Bacteriorhodopsin
	Photocycle},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {5008--5015}
}

@ARTICLE{VALE91,
  author = {Catherine Valentin-Ranc and Marie-France Carlier},
  title = {Role of {ATP}-bound Divalent Metal Ion in the Conformation and Function
	of Actin},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {7668--7675}
}

@ARTICLE{VERR91,
  author = {C.~P.~Verrijzer and J.~A.~W.~M.~van Oosterhout and W.~W.~van Weperen
	and P.~C.~van der Vleit},
  title = {Pou proteins bend {\sc DNA} via the Pou-specific domain.},
  journal = EMBO,
  year = {1991},
  volume = {10},
  pages = {3007--3014},
  annote = {not read ann said there was no bending reported for NF1 in this but
	also it says that pou bends {DNA}eukaryotic sytems}
}

@ARTICLE{VISS91,
  author = {K. J. Visscher and M. C. Chang and F. {van Mourik} and P. S. Parkes-Loach
	and B. A. Heller and P. A. Loach and R. {van Grondelle}},
  title = {Fluorescence Polarization and Low-Temperature Absorption Spectroscopy
	of a Subunit Form of Light-Harvesting Complex I from Purple Photosynthetic
	Bacteria},
  journal = {Biochemistry},
  year = {1991},
  volume = {30},
  pages = {5734--5742}
}

@ARTICLE{VISS91A,
  author = {H.M. Visser and O.J.G. Somsen and F. {van Mourik} and R. {van Grondelle}},
  title = {Excited-state equilibration vie subpicosecond energy transfer within
	the inhomogeneously broadened light-harvesting antenna of {LH}-1-only
	{\em {R}hodobacter sphaeroides} mutants {M}2192 at room tempreature
	and 4.2 {K}},
  journal = {J.~Phys.~Chem.},
  year = {1991},
  volume = {100},
  pages = {18859--1886}
}

@ARTICLE{VRIE91,
  author = {Gerrit Vriend and Chris Sander},
  title = {Detection of Common Three-Dimensional Substructures in Proteins},
  journal = PSFG,
  year = {1991},
  volume = {11},
  pages = {52--58}
}

@ARTICLE{WORG91,
  author = {F. W\"org\"otter and E. Niebur and C. Koch},
  title = {Isotropic Connections Generate Functional Asymmetrical Behavior in
	Visual Cortical Cells},
  journal = {J. Neurophysiology},
  year = {1991}
}

@INCOLLECTION{WALT91,
  author = {J\"org A. Walter and Thomas Martinetz and Klaus Schulten},
  title = {Industrial Robot Learns Visuo-Motor Coordination by Means of ``Neural
	Gas'' Network},
  booktitle = {Artificial Neural Networks},
  publisher = {Elsevier},
  year = {1991},
  editor = {Teuvo Kohonen and Kai M\"akisara and Olli Simula and Jari Kangas},
  pages = {357--364},
  address = {Amsterdam},
  tbtechrep = {TB-91-07}
}

@ARTICLE{WAN91,
  author = {C. Wan and J. Qian and C. K. Johnson},
  title = {Conformational Motion in Bacteriorhodopsin: The {K} to {L} Transition},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {394--400}
}

@UNPUBLISHED{Wang91a,
  author = {D.-L. Wang},
  title = {\mbox{Poisson} Difference Schemes for \mbox{Hamiltonian} Systems
	on Poisson Manifolds},
  note = {Preprint},
  year = {1991}
}

@ARTICLE{Wang91b,
  author = {D.-L. Wang},
  title = {Semi-Discrete Fourier Spectral Approximations for Infinite Dimensional
	\mbox{Hamiltonian} Systems and Conservation Laws},
  journal = {Computers Math. Applic.},
  year = {1991},
  volume = {21},
  pages = {63--75},
  number = {4}
}

@BOOK{WARS91A,
  title = {{Computer Modelling of Chemical Reactions in Enzymes and Solutions}},
  publisher = {John Wiley and Sons, Inc.},
  year = {1991},
  author = {A. Warshel},
  address = {New York}
}

@ARTICLE{WARS91B,
  author = {A. Warshel and J. Aqvist},
  title = {Electrostatic Energy and Macromolecular Function.},
  journal = ARBBC,
  year = {1991},
  volume = {20},
  pages = {267}
}

@ARTICLE{WARS91,
  author = {A.~Warshel and Z.~T.~Chu and J.-K.~Hwang},
  title = {The dynamics of the primary event in rhodopsins revisited},
  journal = CP,
  year = {1991},
  volume = {158},
  pages = {303--314}
}

@ARTICLE{WASZ91,
  author = {B. Waszkowycz and I. H. Hillier and N. Gensmantel and D. W. Payling},
  title = {A quantum Mechanical/Molecular Mechanical Model of Inhibition of
	the enzyme phospholipase {A}$_2$},
  journal = {J. Chem. Soc. Perkin. Trans.},
  year = {1991},
  volume = {2},
  pages = {1819--1832}
}

@ARTICLE{WERY91,
  author = {J. P. Wery and R. W. Schevitz and D. K. Clawson and J. L. Bobbitt
	and E. R. Dow and G. Gamboa and T. {Goodson, Jr.} and R. B. Hermann
	and R. M. Kramer and D. B. McClure and E. D. Mihelich and J. E. Putnam
	and J. D. Sharp and D. H. Stark and C. Teater and M. W. Warrick and
	N. D. Jones},
  title = {Structure of recombinant human rheumatoid arthritic synovial fluid
	phospholipase {A}$_2$ at {2.2\, \AA\ } resolution},
  journal = NAT,
  year = {1991},
  volume = {352},
  pages = {79--82},
  annote = {Lilly paper on PLA2 structure}
}

@ARTICLE{WIEN91,
  author = {Michael C. Wiener and G. I. King and Stephen H. White},
  title = {Structure of a fluid dioleoylphosphatidylcholine bilayer determined
	by joint refinement of x-ray and neutron diffraction data; {I}. Scaling
	of neutron data and the distribution of double-bonds and water},
  journal = BJ,
  year = {1991},
  volume = {60},
  pages = {568--576},
  annote = {requested Tx=19920902.},
  key = {WienerA}
}

@ARTICLE{WIEN91A,
  author = {Michael C. Wiener and Stephen H. White},
  title = {Fluid bilayer structure determination by the combined use of x-ray
	and neutron diffraction; {I}. Fluid bilayer models and the limits
	of resolution},
  journal = BJ,
  year = {1991},
  volume = {59},
  pages = {162--173},
  annote = {LC is the natural state},
  keywords = {LC pghase; quasimolecular model; methods}
}

@ARTICLE{WIEN91B,
  author = {Michael C. Wiener and Stephen H. White},
  title = {Fluid bilayer structure determination by the combined use of x-ray
	and neutron diffraction; {I{}I}. ``Composition-space'' refinement
	method},
  journal = BJ,
  year = {1991},
  volume = {59},
  pages = {174--185},
  annote = {only marginal experimental data on fluid bilayers; describes mainly
	the experimental setup, problems, methods, etc.},
  keywords = {DMPC; composition space; quasimolecular model}
}

@ARTICLE{WILS91,
  author = {C. Wilson and M. R. Wardell and K. H. Weisgraber and R. W. Mahley
	and D. A. Agard},
  title = {Three-Dimensional Structure of the {LDL} Receptor-Binding Domain
	of Human Apolipoprotein {E}},
  journal = SCI,
  year = {1991},
  volume = {252},
  pages = {1817--1822}
}

@ARTICLE{WIND91A,
  author = {Andreas Windemuth and Klaus Schulten},
  title = {Molecular Dynamics Simulation on the {C}onnection {M}achine},
  journal = MS,
  year = {1991},
  volume = {5},
  pages = {353--361}
}

@TECHREPORT{WIND91B,
  author = {Andreas Windemuth and Klaus Schulten},
  title = {Stochastic Dynamics Simulation for Macromolecules},
  institution = {University of Illinois},
  year = {1991},
  type = {Beckman Institute Technical Report},
  number = {TB-91-19},
  annote = {This was only published as a technical report, never as a journal
	article.},
  tbtechrep = {TB-91-19}
}

@UNPUBLISHED{WiSc91,
  author = {A. Windemuth and K. Schulten},
  title = {Stochastic Dynamics Simulation for Macromolecules},
  note = {manuscript},
  year = {1991}
}

@ARTICLE{WiHo91,
  author = {J. Wisdom and Holman},
  title = {Symplectic Maps for the N-Body Problem},
  journal = {Astr.\ J.},
  year = {1991},
  volume = {102},
  pages = {1528--1538},
  number = {4},
  nremark = { "\% in BI files??, MQZ: I think ASTRONOMICAL-JOURNAL is in physics
	library.", WiHT96: ``construction of higher order mappings through
	delta function formulation''}
}

@BOOK{WOLF91,
  title = {Mathematica, A System for Doing Mathematics by Computer},
  publisher = {Ad\-di\-son-Wesley},
  year = {1991},
  author = {Stephen Wolfram},
  address = {New York},
  edition = {2}
}

@ARTICLE{WRIG91A,
  author = {A.~P.~H.~Wright and J.~Gustafsson},
  title = {Mechanism of synergistic transcriptional transactivation by the human
	glucocorticoid receptor},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {8283--8287},
  annote = { protein-protein interactions in the T1 domain mediate cooperative
	DNA-binding, T1 and T2 are transactivation domains and T1 is the
	sole determinant of synergetic transactivation by the receptor }
}

@ARTICLE{WRIG91,
  author = {S. M. Wright and R. L. Magin and J. R. Kelton},
  title = {Arrays of mutually coupled receiver coils: Theory and application},
  journal = {Magn. Reson. Med.},
  year = {1991},
  volume = {17},
  pages = {252--268}
}

@ARTICLE{WU91,
  author = {Jogin R. Wu and Barry R. Lentz},
  title = {Mechanism of Poly(ethylene glycol)-Induced Lipid Transfer between
	Phosphatidylcholine Large Unilamellar Vesicles: A Fluorescent Probe
	Study},
  journal = BCH,
  year = {1991},
  volume = {30},
  pages = {6780--6787}
}

@ARTICLE{WU91A,
  author = {S. Wu and M. A. El-Sayed},
  title = {{CD} Spectrum of Bacteriorhodopsin},
  journal = BJ,
  year = {1991},
  volume = {60},
  pages = {190--197}
}

@ARTICLE{YAN91,
  author = {B. Yan and J. Spudich},
  title = {Evidence that the Repellent Receptor Form of Sensory Rhodopsin I
	is an Attractant Signaling State},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1023--1026}
}

@ARTICLE{Yang91,
  author = {Weitao Yang},
  title = {Direct Calculation of Electron Density in Density-Functional Theory},
  journal = {Phys.\ Rev.\ Lett.},
  year = {1991},
  volume = {66},
  pages = {1438}
}

@ARTICLE{YoKu91,
  author = {T. Yoshizawa and O. Kuwata},
  title = {Iodopsin, a Red-sensitive Cone Visual Pigment in the Chicken Retina},
  journal = JPP,
  year = {1991},
  volume = {54},
  pages = {1061--1070}
}

@ARTICLE{ZHAO91,
  author = {F. Zhao and S. L. Johnsson},
  title = {The parallel multipole method on the Connection Machine},
  journal = {SIAM L. Sci, Stat. Comp.},
  year = {1991},
  volume = {12},
  pages = {1420}
}

@ARTICLE{ZhJo91,
  author = {F. Zhao and S. L. Johnsson},
  title = {The Parallel Multipole Method on the Connection Machine},
  journal = SJSSC,
  year = {1991},
  volume = {12},
  pages = {1420--1437}
}

@ARTICLE{ZHUK91,
  author = {E.~A. Zhukovsky and P.~R. Robinson and D.~O. Oprian},
  title = {Transducin Activation by Rhodopsin Without a Covalent Bond to the
	11-{\it Cis}-Retinal Chromophore},
  journal = SCI,
  year = {1991},
  volume = {251},
  pages = {558--560}
}

@ARTICLE{ZILL91,
  author = {J.~Zilliacus and K.~Dahlman--Wright and A.~Wright and J.~Gustafsson
	and J.~Carlstedt-Duke },
  title = {{DNA}--binding specificity of mutant glucocorticoid receptor {DNA}--binding
	domains.},
  journal = JBC,
  year = {1991},
  volume = {266},
  pages = {3101--3106},
  annote = {experimental study showing that not only the P-box residues are involved
	in binding specificity}
}

@INPROCEEDINGS{ZUBE91,
  author = {H. Zuber and R.A. Brunisholz},
  title = {Structure and Function of Antenna Polypeptides and Chlorophyll-Protein
	Complexes: Principles and Variability},
  booktitle = {Chlorophylls},
  year = {1991},
  editor = {H. Scheer},
  pages = {627--692},
  address = {Boca Raton},
  publisher = {CRC Press}
}

@MASTERSTHESIS{BOEH90A,
  author = {Klaus Boehncke},
  title = {{W}echselwirkung zwischen {DNA} und dem {P}harmakon {D}istamycin},
  school = {{T}echnische {U}niversit\"at {M}\"unchen, {P}hysik-Department, T~30},
  year = {1990},
  type = {Diploma Thesis},
  address = {James-Franck-Stra{\ss}e, 8046~Garching},
  month = APR
}

@TECHREPORT{MAY90,
  author = {David May and Peter Thompson},
  title = {Transputers and Routers: Components for Concurrent Machines},
  institution = {{INMOS}},
  year = {1990},
  month = APR
}

@ARTICLE{DEGR90,
  author = {H. J. M. {de Groot} and S. O. Smith and J. Courtin and E. {van den
	Berg} and C. Winkel and J. Lugtenburg and R. G. Griffin and J. Herzfeld},
  title = {Solid-state $^{13}${C} and $^{15}${N} {NMR} Study of the Low {pH}
	Forms of Bacteriorhodopsin},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {6873--6883}
}

@ARTICLE{Sali90,
  author = {Andrej {\v S}ali and Tom L. Blundell},
  title = {Definition of General Topological Equivalence in Protein Structures},
  journal = JMB,
  year = {1990},
  volume = {212},
  pages = {403--428}
}

@TECHREPORT{AbSa90,
  author = {L. Abia and J. M. Sanz-Serna},
  title = {\mbox{Partitioned Runge-Kutta} methods for separable \mbox{Hamiltonian}
	problems},
  institution = {Universidad de Valladolid},
  year = {1990},
  number = {1990/8},
  address = {Valladolid, Spain}
}

@ARTICLE{ALTS90,
  author = {S.~F.~Altschul and W.~Gish and W.~Miller and E.~W.~Myers and D.~J.~Lipman},
  title = {Basic local alignment search tool},
  journal = JMB,
  year = {1990},
  volume = {215},
  pages = {403--410}
}

@ARTICLE{Tera,
  author = {R. Alverson and D. Callahan and D. Cummings and B. Koblenz and A.
	Porterfield and B. Smith},
  title = {The Tera Computer System},
  journal = {Proceedings of the ACM International Conference on Supercomputing,
	Amsterdam, The Netherlands},
  year = {1990}
}

@ARTICLE{ANDE90,
  author = {Bryan F. Anderson and Heather M. Baker and Gillian E. Norris and
	Sylvia V. Rumball and Edward N. Baker},
  title = {Apolactoferrin structure demonstrates ligand-induced conformational
	change in transferrins},
  journal = NAT,
  year = {1990},
  volume = {344},
  pages = {784--787}
}

@ARTICLE{ANDE90A,
  author = {D. E. Anderson and Wayne J. Becktel and F. W. Dahlquist},
  title = {p{H}-{Induced} denaturation of proteins: A single saltbridge contributes
	3-5 kcal/mol to the free energy of folding of {T4} lysozyme},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {2403--2408}
}

@BOOK{ArPl90,
  title = {An Introduction to Dynamical Systems},
  publisher = {Cambridge University Press},
  year = {1990},
  author = {D.~K.~Arrowsmith and C.~M.~Place},
  address = {Cambridge},
  nremark = {423 p., CALL NO: 515.352AR69I, SUBJECT: Differentiable dynamical systems,
	ISBN: 0521303621, 0521316502 (pbk.)}
}

@ARTICLE{AsMS90,
  author = {Steven F. Ashby and Thomas A. Manteuffel and Paul E. Saylor},
  title = {A Taxonomy for Conjugate Gradient Methods},
  journal = SJNA,
  year = {1990},
  volume = {27},
  pages = {1542--1568},
  number = {6}
}

@ARTICLE{AMKJ90,
  author = {F. Avbelj and J. Moult and H. Kitson and M. James and A. Hagler},
  title = {Molecular Dynamics Study of the Structure and Dynamics of a Protein
	Molecule in Crystalline Ionic Environment, Streptomyces Griseus Protease
	A},
  journal = {Biochemistry},
  year = {1990},
  volume = {29},
  pages = {8658--8679}
}

@ARTICLE{BADE90,
  author = {J. S. Bader and R. A. Kuharski and D. Chandler},
  title = {Role of Nuclear Tunneling in Aqueous Ferrous-Ferric Electron Transfer},
  journal = JCP,
  year = {1990},
  volume = {93},
  pages = {230--236}
}

@MISC{BARR90,
  author = {Iann Barron},
  title = {What is Virtual Reality?},
  year = {1990},
  note = {promotional materials},
  organization = {{DIVISION} Ltd.}
}

@ARTICLE{BASH90,
  author = {Donald Bashford and Martin Karplus},
  title = {{pK}$_{{\rm a}}$'s of Ionizable Groups in Proteins: Atomic Detail
	from a Continuum Electrostatic Model},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {10219--10225}
}

@ARTICLE{BAZA90,
  author = {J. Fernando Bazan},
  title = {Structural design and molecular evolution of a cytokine receptor
	superfamily},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {6934--6938}
}

@ARTICLE{BEKK90,
  author = {H. Bekker and M. Renardus},
  title = {Design of a transputer network for searching neighbors in {M.D.}
	simulations},
  journal = MM,
  year = {1990},
  volume = {30},
  pages = {159--166}
}

@ARTICLE{BERT90,
  author = {A. Bertazzon and G. H. Tian and A. Lamblin and Tian Yow Tsong},
  title = {Enthalpic and Entropic Contributions to Actin Stability: Calorimetry,
	Circular Dichroism, and Fluorescence Study and Effects of Calcium},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {291--298}
}

@ARTICLE{BESL90,
  author = {B. H. Besler and K. M. Merz and P. A. Kollman},
  title = {Atomic Charges Derived From Semiempirical Methods},
  journal = JCC,
  year = {1990},
  volume = {11},
  pages = {431--439}
}

@ARTICLE{BIRG90,
  author = {R. R. Birge},
  title = {Photophysics and Molecular Electronic Applications of the Rhodopsins},
  journal = ARP,
  year = {1990},
  volume = {41},
  pages = {683--733}
}

@ARTICLE{BIRG90A,
  author = {R. R. Birge},
  title = {Nature of the Primary Photochemical Event in Rhodopsin and Bacteriorhodopsin},
  journal = BBA,
  year = {1990},
  volume = {1016},
  pages = {293--327}
}

@ARTICLE{BIRGE90,
  author = {R.~R.~Birge},
  title = {Photophysics and molecular electronic applications of the rhodopsins},
  journal = {Ann. Rev. Phys. Chem.},
  year = {1990},
  volume = {41},
  pages = {683--733}
}

@ARTICLE{BIRG90B,
  author = {R.\ R.\ Birge and C.\ F.\ Zhang},
  title = {Two Photon Spectroscopy of Light Adapted Bacteriorhodopsin},
  journal = JCP,
  year = {1990},
  volume = {92},
  pages = {7178--7195}
}

@ARTICLE{BITT90,
  author = {Robert Bittl and Klaus Schulten},
  title = {Biradical Spin Dynamics with Distance-Dependent Exchange Interaction
	and Electron Transfer Efficiency},
  journal = CPL,
  year = {1990},
  volume = {173},
  pages = {387--392}
}

@ARTICLE{BITT90A,
  author = {Robert Bittl and Klaus Schulten and Nick Turro},
  title = {Micellar Radical Pair Decay},
  journal = JCP,
  year = {1990},
  volume = {93},
  pages = {8260--8269}
}

@ARTICLE{BLOC90,
  author = {S.M. Block and L.S. Goldstein and B.J. Schnapp},
  title = {Bead movement by single kinesin molecules studied with optical tweezers},
  journal = NAT,
  year = {1990},
  volume = {348},
  pages = {348--352}
}

@INPROCEEDINGS{BOAR90B,
  author = {Board, Jr., J. A. and R. R. Batchelor and Leathrum, Jr., J. F.},
  title = {High Performance Implementations of the Fast Multipole Algorithm},
  booktitle = {Symposium on Parallel and Vector Computation in Heat Transfer, Proc.
	1990 AIAA/ASME Thermophysics and Heat Transfer Conference},
  year = {1990},
  annote = {requested Tx=19930129. by H. Heller}
}

@INPROCEEDINGS{BOAR90,
  author = {Board, Jr., John A. and Leathrum, Jr., James F.},
  title = {The Fast Multipole Algorithm on Transputer Networks},
  booktitle = {Transputer Research and Applications 3, NATUG-3 Proceedings},
  year = {1990},
  editor = {Alan S. Wagner},
  pages = {63--74},
  address = {Amsterdam},
  organization = {The North American Transputer Users Group},
  publisher = {IOS Press}
}

@INPROCEEDINGS{BOEH90,
  author = {Klaus Boehncke and Helmut Heller and Helmut Grubm{\"u}ller and Klaus
	Schulten},
  title = {Molecular Dynamics Simulations on a Systolic Ring of Transputers},
  booktitle = {{NATUG~3:} Transputer Research and Applications~3},
  year = {1990},
  editor = {Alan S. Wagner},
  pages = {83--94},
  address = {Amsterdam},
  organization = {North American Transputer Users Group},
  publisher = {{IOS} Press},
  annotes = {Proceedings of the Third Conference of the North American Transputer
	Users Group, April~26--27, 1990 --- Sunnyvale, CA}
}

@ARTICLE{BOWY90,
  author = {Bowyer, J. and Hilton, M. and Whitelegge and Jewess, P. and Camilleri,
	P. and Crofts, A. and Robinson, H.},
  title = {Calculation of deformation energies and conformations in lipid membranes
	containing gramicidin channels},
  journal = {Z. Naturforsch.},
  year = {1990},
  volume = {45c},
  pages = {379--387},
  annote = {requested Tx=19920924.}
}

@ARTICLE{BrLu90,
  author = {A. Brandt and A. A. Lubrecht},
  title = {Multilevel Matrix Multiplication and Fast Solution of Integral Equations},
  journal = {J. Comput. Phys.},
  year = {1990},
  volume = {90},
  pages = {348--370}
}

@ARTICLE{BRAS90a,
  author = {R. Brasseur and J. De Meutter and B. Vanloo and E. Goormaghtigh and
	J.-M. Ruysschaert and M. Rosseneu},
  title = {Mode of Assembly of Amphipathic Helical Segments in Model High-Density
	Lipoproteins},
  journal = BBA,
  year = {1990},
  volume = {1043},
  pages = {245--252}
}

@ARTICLE{BRYN90,
  author = {J. D. Bryngelson and P. G. Wolynes},
  title = {A Simple Statistical Field Theory of Heteropolymer Collapse with
	Application to Protein Folding},
  journal = {Biopolymers},
  year = {1990},
  volume = {30},
  pages = {177}
}

@ARTICLE{BRUN90,
  author = {Axel Br{\"u}nger},
  title = {Extension of Molecular Replacement: A New Search Strategy Based on
	{P}atterson Correlation Refinement},
  journal = {\it Acta Cryst.},
  year = {1990},
  volume = {A46},
  pages = {46--57}
}

@MANUAL{BRUN90a,
  title = {{X-PLOR}, Version~2.1},
  author = {Axel T. Br{\"u}nger},
  organization = {The Howard Hughes Medical Institute and Department of Molecular Biophysics
	and Biochemistry, Yale University},
  address = {260 Whitney Avenue, P.O. Box~6666, New Haven, CT~06511},
  year = {1990}
}

@ARTICLE{BRUN90b,
  author = {A. T. Br{\"u}nger and A. Krukowski and J. Erickson},
  title = {Slow-Cooling Protocols for Crystallographic Refinement by Simulated
	Annealing},
  journal = {\it Acta Cryst.},
  year = {1990},
  volume = {A46},
  pages = {585--593}
}

@BOOK{BUTK90,
  title = {Control of quantum-mechanical processes and systems},
  publisher = {Kluwer Academic Publishers},
  year = {1990},
  author = {A. G. Butkovskii and Y. I. Samoilenko},
  address = {Boston}
}

@ARTICLE{BUTT90,
  author = {H. Butt and K. H. Downing and P. K. Hansma},
  title = {Imaging the Membrane Protein Bacteriorhodopsin With the Atomic Force
	Microscope},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {1473--1480}
}

@ARTICLE{CaBe90,
  author = {J. Cao and B. J. Berne},
  title = {{M}onte {C}arlo Methods for Accelerating Barrier Crossing: Anti-Force-Bias
	and Variable Step Algorithms},
  journal = {J. Chem. Phys.},
  year = {1990},
  volume = {92},
  pages = {1980}
}

@ARTICLE{CHAN88,
  author = {P. J. Channell and J. C. Scovel},
  title = {Symplectic Integration of {Hamiltonian} Systems},
  journal = {Nonlinearity},
  year = {1990},
  volume = {3},
  pages = {231--259},
  number = {2}
}

@ARTICLE{ChSc90,
  author = {P. J. Channell and J. C. Scovel},
  title = {Symplectic Integration of \mbox{Hamiltonian} Systems},
  journal = {Nonlinearity},
  year = {1990},
  volume = {3},
  pages = {231--259}
}

@ARTICLE{CHU90B,
  author = {S. C.-K. Chu and Y. Xu and J. A. Balschi and C. S. Springer Jr.},
  title = {Bulk Magnetic Susceptability Shifts in {NMR} Studies of Compartementalized
	Samples: Use of Paramagnetic Reagents},
  journal = MRM,
  year = {1990},
  volume = {{\bf 13}},
  pages = {239--262},
  brief = {This paper considers only frequncy SHIFTS, rather than relaxation
	rate enhancements, so it is irrelevant for our purposes. Gives suscept.
	values for water and reference for that of Gd-DTPA},
  keywords = {frequency shifts}
}

@INPROCEEDINGS{CHU90,
  author = {W. C. Chu and C. B. Ahn and Z. H. Cho},
  title = {{M}onte {C}arlo Simulation of Diffusion in {NMR} Microscopy},
  booktitle = {Book of Abstracts},
  year = {1990},
  volume = {1},
  pages = {394},
  organization = smrm,
  annote = {and references therein},
  brief = {1\,$\mu$m resolution is possible if Diff-const not too high}
}

@ARTICLE{CIEP90,
  author = {P. Ciepak and S. N. Rao and P. D.~J. Grootenhuis and P. A. Kollman},
  title = {Free Energy Calculation on Base Specificity of Drug-{DNA} Interactions:
	Application to Daunomycin and Acridine Intercalation into {DNA}},
  journal = BP,
  year = {1990},
  volume = {29},
  pages = {717--727}
}

@ARTICLE{COHE90,
  author = {N.C. Cohen and J.M. Blaney and C. Humblet and P. Gund and D.C. Barry},
  title = {Molecular Modeling Software and Methods for Medicinal Chemistry},
  journal = JMC,
  year = {1990},
  volume = {33},
  pages = {883--894}
}

@ARTICLE{COLL90,
  author = {John Collins and Michael Szardenings and Friedhelm Maywald and Helmut
	Bl{\"o}cker and Ronald Frank and Hans-J{\"u}rgen Hecht and Birger
	Vasel and Dietmar Schomburg and Edwin Fink and Hans Fritz},
  title = {Human Leukocyte Elastase Inhibitors: Designed Variants of Human Pancreatic
	Secretory Trypsin Inhibitor {(hPSTI)}},
  journal = BCHS,
  year = {1990},
  volume = {371, suppl},
  pages = {29--36},
  annote = {one of the first works, where CAPD really helped to improve the drug
	(inhibitor); design of the inhibitor on the basis of a similar one},
  keywords = {computer aided protein design CAPD; BRAGI; ARGOS}
}

@ARTICLE{COSG90,
  author = {S. A. Cosgrove and M. A. Guite and T. B. Burnell and R. L. Christiensen},
  title = {Electronic Relaxation in Long Polyenes},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {8118--8124}
}

@ARTICLE{CRIC90,
  author = {Francis Crick and Christof Koch},
  title = {Towards a neurobiological theory of consciousness},
  journal = {Sem. Neurosci.},
  year = {1990},
  volume = {2},
  pages = {263--275}
}

@ARTICLE{CUSA90,
  author = {S. Cusack and W. Doster},
  title = {Temperature Dependence of the Low Frequency Dynamics of Myoglobin
	-- Measurement of the Vibrational Frequency Distribution by Inelastic
	Neutron Scattering},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {243--251}
}

@ARTICLE{WRIG90,
  author = {Karin Dahlman-Wright and Helmi Siltala-Roos and Jan Carlstedt-Duke
	and J.~Gustafsson},
  title = {Protein-Protein Interactions Facilitate {\sc DNA} Binding by the
	Glucocorticoid Receptor {\sc DNA}-binding Domain},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {14030--14035},
  annote = {should also be included with any ref to ERIK90, specificity of one
	site greater than other can affect the binding, has relevance to
	why sigler's trick worked, hormone will bind to degenerated backbone,
	see also ERIK90,WRIG91a}
}

@ARTICLE{DANC90,
  author = {Peter Dancker and Lore Hess},
  title = {Phalloidin reduces the release of inorganic phosphate during actin
	polymerization},
  journal = BBA,
  year = {1990},
  volume = {1035},
  pages = {197--200}
}

@BOOK{DARN90,
  title = {Molecular Cell Biology},
  publisher = {W. H. Freeman and Co.},
  year = {1990},
  author = {James E. Darnell and Harvey Lodish and David Baltimore},
  addrerss = {New York},
  annote = {has many very artistic pictures of cells. cell-plant-darnell.tiff
	from page 115; cell-animal-darnell.tiff from page 113; liposome-darnell.tiff
	from page 77; micelle-darnell.tiff from page 77; membrane-darnell.tiff
	from page 77}
}

@ARTICLE{DAVI90,
  author = {Malcolm E.\ Davis and Andrew McCammon},
  title = {Electrostatics in Biomolecular Structure and Dynamics},
  journal = {Chem.\ Rev.},
  year = {1990},
  volume = {90},
  pages = {509--521}
}

@ARTICLE{DaMc90,
  author = {Davis, M. E. and McCammon, J. A.},
  title = {Electrostatics in Biomolecular Structure and Dynamics},
  journal = {Chem.\ Rev.},
  year = {1990},
  volume = {90},
  pages = {509}
}

@ARTICLE{DEMA90,
  author = {J. P. Demaret and S. Brunie},
  title = {Molecular dynamics simulations of phospholipase {A}$_2$},
  journal = {Protein Engineering},
  year = {1990},
  volume = {4},
  pages = {163--170}
}

@ARTICLE{DENC90,
  author = {N. A. Dencher and G. Papadopoulos and D. Dresselhaus and G. B{\"u}ldt},
  title = {Light- and Dark-Adapted Bacteriorhodopsin, a Time-Resolved Neutron
	Diffraction Study},
  journal = BBA,
  year = {1990},
  volume = {1026},
  pages = {51--56}
}

@ARTICLE{DIAM90,
  author = {R. Diamond},
  title = {On the factorization of rotations with examples in diffractometry},
  journal = PRSLA,
  year = {1990},
  volume = {428},
  pages = {451--472}
}

@INCOLLECTION{DIVK90,
  author = {Robert Divko and Klaus Schulten},
  title = {Hierarchical Spin Model for Stereo Interpretation Using Phase Sensitive
	Detectors},
  booktitle = {Parallel Processing in Neural Systems and Computers},
  publisher = {Elsevier},
  year = {1990},
  editor = {R. Eckmiller and G. Hartmann and G. Hauske},
  pages = {335--338},
  address = {Amsterdam},
  annote = {This book is contains the proceedings of the Int. Conf. on Parallel
	Processing in Neural Systems and Computers {(ICNC)}, D\"usseldorf,
	March 1990}
}

@BOOK{DoMa90,
  title = {Introduction to Differential Geometry for Engineers},
  publisher = {Marcel Dekker, Inc.},
  year = {1990},
  author = {B. F. Doolin and C. F. Martin},
  nremark = {ISBN: 0-8247-8396-4 see publisher files},
  place = {New York}
}

@ARTICLE{DU90,
  author = {P. Du and R. Davidson},
  title = {Ab Initio Study on the Excitation Energies of the Protonated Schiff
	Base of 11-cis-Retinal},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {7013--1020}
}

@ARTICLE{DU89,
  author = {P. Du and S. C. Racine and R. Davidson},
  title = {Theoretical Study of the Excitations Energies of Methaniminium Cation,
	Propeniminium Cation, and Propenimine},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {3944--3951}
}

@ARTICLE{DURB90,
  author = {R. Durbin and G. Mitchinson},
  title = {A Dimension Reduction Framework for Understanding Cortical Maps},
  journal = NAT,
  year = {1990},
  volume = {343},
  pages = {644--647}
}

@ARTICLE{EARN90,
  author = {T. N. Earnest and J. Herzfeld and K. J. Rothschild},
  title = {Polarized {Fourier} Transform Infrared Spectroscopy of Bacteriorhodopsin},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {1539--1546}
}

@ARTICLE{EGGE90,
  author = {M. Egger and F. Ohnesorge and A. L. Weisenhorn and S. P. Heyn and
	B. Drake and C. B. Prater and S. A. C. Gould and P. K. Hansma and
	Hermann E. Gaub},
  title = {Wet Lipid--Protein Membranes Imaged at Submolecular Resolution by
	Atomic Force Microscopy},
  journal = JSB,
  year = {1990},
  volume = {103},
  pages = {89--94},
  annote = {chain tilt=30^o \pm 5^o versus normal; area/headgroup = 45\pm19A^2},
  keywords = {DMPG; experimental; membrane; force microscope (AFM)},
  suggestions = {produce image analog to Fig2 here (view from above on headgroups (dark),
	no water, hydrocarbon with a lighter color)}
}

@ARTICLE{EGLO90,
  author = {Eglowstein, H.},
  title = {Reach Out and Touch Your Data},
  journal = {Byte},
  year = {1990},
  pages = {283--290}
}

@TECHREPORT{EiSS90,
  author = {T. Eirola and J. M. Sanz-Serna},
  title = {Conservation of Integrals and Symplectic Structure in the Integration
	of Differential Equations by Multistep Methods},
  institution = {Universidad de Valladolid},
  year = {1990},
  number = {1990/9},
  address = {Valladolid, Spain}
}

@ARTICLE{ELBE90A,
  author = {R. Elber},
  title = {Calculation of the potential of mean force using molecular dynamics
	with linear constraints: An application to a conformational transition
	in a solvated dipeptide},
  journal = JCP,
  year = {1990},
  volume = {93},
  pages = {4312--4321}
}

@ARTICLE{ELBE90,
  author = {R. Elber and M. Karplus},
  title = {Enhanced Sampling in Molecular Dynamics: Use of the Time-Dependent
	{Hartree} Approximation for a Simulation of Carbon Monoxide Diffusion
	through Myoglobin},
  journal = JACS,
  year = {1990},
  volume = {112},
  pages = {9161--9175},
  number = {25}
}

@ARTICLE{ENGE90,
  author = {M. Engelhard and B. Hess and G. Metz and W. Kreutz and F. Siebert
	and J. Soppa and D. Oesterhelt},
  title = {High Resolution $^{13}${C}-Solid State {NMR} of Bacteriorhodopsin:
	Assignment of Specific Aspartic Acids and Structural Implications
	of Single Site Mutations},
  journal = EBJ,
  year = {1990},
  volume = {18},
  pages = {17--24}
}

@ARTICLE{ERIK90,
  author = {P.~Eriksson and {\"O}.~Wrange},
  title = {Protein--Protein Contacts in the Glucocorticoid Receptor Homodimer
	Influence Its {DNA} Binding Properties},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {3535--3542},
  annote = {gives the details of protein--protein contacts also is a good ref
	for protein-dna contacts, consider full receptor and fragements,
	DBD, general GR and hormone information, include with ref to WRIG90}
}

@ARTICLE{FeWQ90,
  author = {K. Feng and H.-M. Wu and M.-Z. Qin},
  title = {Symplectic Difference Schemes for Linear \mbox{Hamiltonian} Canonical
	Systems},
  journal = {J. Comput. Math.},
  year = {1990},
  volume = {8},
  pages = {371--380},
  number = {4}
}

@ARTICLE{FIEL90,
  author = {M. J. Field and P. A. Bash and M. Karplus},
  title = {A Combined Quantum Mechanical and Molecular Mechanical Potential
	for Molecular Dynamics Simulations},
  journal = JCC,
  year = {1990},
  volume = {11},
  pages = {700--733},
  number = {6}
}

@ARTICLE{FLAH90,
  author = {Kevin M. Flaherty and Camille DeLuca-Flaherty and David B. McKay},
  title = {Three-dimensional structure of the {ATP}ase fragment of a 70{K} heat-shock
	cognate protein},
  journal = NAT,
  year = {1990},
  volume = {346},
  pages = {623--628}
}

@BOOK{FOLE90,
  title = {Computer Graphics, Principles and Practices},
  publisher = {Addison-Wesley},
  year = {1990},
  author = {Foley, J. and van Dam, A. and Feiner, S. and Hughes, J.},
  address = {New York}
}

@ARTICLE{FoRu90,
  author = {E. Forest and R. D Ruth},
  title = {Fourth-Order Symplectic Integration},
  journal = {Physica D},
  year = {1990},
  volume = {43},
  pages = {105--117}
}

@ARTICLE{FrFD90,
  author = {D. D. Frantz and D. L. Freeman and J. D. Doll},
  title = {Reducing Quasi-ergodic Behavior in {M}onte {C}arlo Simulation by
	{J}-walking: Applications to Atomic Clusters},
  journal = {J. Chem.\ Phys.},
  year = {1990},
  volume = {93},
  pages = {2769}
}

@ARTICLE{FRIE90,
  author = {M. S. Friedrichs and P. G. Wolynes},
  title = {Molecular Dynamics of Associative Memory {Hamiltonian}s for Protein
	Tertiary Structure Recognition},
  journal = {Tetrahedron Computer Methodology},
  year = {1990},
  volume = {3},
  pages = {175}
}

@ARTICLE{GART90,
  author = {M.~R.~Gartenberg and C.~Ampe and T.~A.~Steitz and D.~M.~Crothers},
  title = {Molecular characterization of the {\sc GCN4-DNA} complex.},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {6034--6038},
  annote = {GCN4 does not bend DNA,have not read it}
}

@TECHREPORT{GEIS90,
  author = {G. A. Geist and M. T. Heath and B. W. Peyton and P. H. Worley},
  title = {PICL: a portable instrumented communication library, C reference
	manual},
  institution = {Oak Ridge National Laboratory},
  year = {1990},
  number = {ORNL/TM-11130}
}

@ARTICLE{GERW90,
  author = {K. Gerwert and G. Souvignier and B. Hess},
  title = {Simultaneous Monitoring of Light-Induced Changes in Protein Side-Group
	Protonation, Chromophore Isomerization, and Backbone Motion of Bacteriorhodopsin
	by Time-Resolved {Fourier}-Transform Infrared Spectroscopy},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {9774--9778}
}

@ARTICLE{GIBR90,
  author = {J.F. Gibrat and N. G${\bar {\rm o}}$},
  title = {Normal Mode Analysis of Human Lysozyme: {Study} of the Relative Motion
	of the Two Domains and Characterization of Harmonic Motion},
  journal = {Proteins: Structure, Function, and Genetics},
  year = {1990},
  volume = {8},
  pages = {258--279}
}

@ARTICLE{GILB90,
  author = {C. D. Gilbert and T. N. Wiesel},
  title = {The Influence of Contextual Stimuli on the Orientation Selectivity
	of Cells in Primary Visual Cortex of the Cat.},
  journal = {Vis. Res.},
  year = {1990},
  volume = {30},
  pages = {1689--1703}
}

@ARTICLE{GLAS90,
  author = {C.~K.~Glass and J.~M.~Holloway},
  title = {Regulation of gene expression by the thyroid hormone receptor.},
  journal = BBA,
  year = {1990},
  volume = {1032},
  pages = {157--176}
}

@ARTICLE{GOVI90,
  author = {R.~Govindjee and S.~P.~Balashov and T.~G.~Ebrey},
  title = {Quantum efficiency of the photochemical cycle of bacteriorhodopsin},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {597--608}
}

@INPROCEEDINGS{GRAA90,
  author = {Jang F. M. Graat},
  title = {Dynamic parallel programming},
  booktitle = {Transputer Research and Applications 3, {NATUG-3} Proceedings},
  year = {1990},
  editor = {Alan S. Wagner},
  address = {Amsterdam},
  organization = {The North American Transputer Users Group},
  publisher = {IOS Press},
  keywords = {Transputer}
}

@INCOLLECTION{GREE90a,
  author = {N. M. Green},
  title = {Avidin and Streptavidin},
  booktitle = ME,
  publisher = {Academic Press},
  year = {1990},
  editor = {M. Wilcheck and E. A. Bayer},
  volume = {184},
  pages = {51--67},
  address = {London}
}

@ARTICLE{Gree90,
  author = {D. Greenspan},
  title = {Conservative Difference Formulations of \mbox{Calogero} and \mbox{Toda
	Hamiltonian} Systems},
  journal = {Comput. Math. Applic.},
  year = {1990},
  volume = {29},
  pages = {91--95}
}

@INPROCEEDINGS{GROS90,
  author = {Guenter W. Gross and Jacek Kowalski},
  title = {Experimental and Theoretical Analysis of Random Nerve Cell Network
	Dynamics},
  booktitle = {Neural Networks: Concepts, Applications, and Implementations},
  year = {1990},
  editor = {P. Antognetti and V. Milutinovic},
  volume = {3},
  address = {Englewood Cliffs, NJ},
  publisher = {Prentice Hall}
}

@ARTICLE{GROSS90,
  author = {Michael F. Grossjean and Paul Tavan and Klaus Schulten},
  title = {Quantum Chemical Vibrational Analysis of the Chromophore of Bacteriorhodopsin},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {8059--8069}
}

@INPROCEEDINGS{GUNS90A,
  author = {W. F. van Gunsteren},
  title = {On Testing Theoretical Models by Comparision of Calculated with Experimental
	Data},
  booktitle = {Modelling of Molecular Structures and Properties},
  year = {1990},
  editor = {J.-L. Rivail},
  volume = {71},
  series = {Studies in Physical and Theoretical Chemistry},
  pages = {463--478},
  address = {Amsterdam},
  publisher = {Elsevier Science Publishers},
  note = {Proceedings of an International Meeting},
  annote = {Good general remarks on model testing. Examples of unwanted error
	compensation, also on MD algorithms.},
  keywords = {accuracy}
}

@ARTICLE{GuBe90,
  author = {W.~F.~van Gunsteren and Berendsen, H.~J.~C.},
  title = {Computer Simulation of Molecular Dynamics: Methodology, Applications
	and Perspectives in Chemistry},
  journal = {Chemie Int. Ed. Engl.},
  year = {1990},
  volume = {29},
  pages = {922--1023},
  nremark = {comment="a review from van Gunsteren, article really has something
	to do with Brownian dynamics", comment??=" Angewandte", GROMOS96}
}

@ARTICLE{GUNS90,
  author = {Wilfred F. van Gunsteren and Herman J. C. Berendsen},
  title = {{M}olek\"uldynamik-{C}om\-put\-er\-sim\-u\-la\-tionen; {M}ethodik,
	{A}n\-wen\-dun\-gen und {P}er\-spek\-tiven in der {C}hemie},
  journal = {Angew. Chemie},
  year = {1990},
  volume = {102},
  pages = {1020--1055}
}

@ARTICLE{GIKP90,
  author = {S. Gupta and A. Irb{\"a}ck and F. Karsch and B. Petersson},
  title = {The Acceptance Probability in the Hybrid {M}onte-{C}arlo Method},
  journal = PLB,
  year = {1990},
  volume = {242},
  pages = {437--443}
}

@ARTICLE{GUY90,
  author = {H. R. Guy and F. Conti},
  title = {pursuing the structure and function of voltage-gated channel},
  journal = TINS,
  year = {1990},
  volume = {13},
  pages = {201--206}
}

@ARTICLE{HAN90,
  author = {Xianlin Han and Richard W. Gross},
  title = {Plasmenylcholine and Phosphatidylcholine Membrane Bilayers Possess
	Distinct Conformational Motifs},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {4992--4996},
  annote = {experimental, not simulation; Gross works with Garland Marshall in
	St. Louis}
}

@ARTICLE{HARR90,
  author = {S. C. Harrison and A. K. Aggarwal},
  title = {{DNA} Recognition by Proteins With the Helix-Turn-Helix Motif},
  journal = {Annu.\ Rev.\ Biochem.},
  year = {1990},
  volume = {59},
  pages = {933--969}
}

@ARTICLE{HAUS90,
  author = {T. Hauss and S. Grzesiek and H. Otto and J. Westerhausen and M. P.
	Heyn},
  title = {Transmembrane Location of Retinal in Bacteriorhodopsin by Neutron
	Diffraction},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {4904--4913}
}

@ARTICLE{HAYE90,
  author = {J.~J.~Hayes and D.~Clark and A.~P.~Wolffe},
  title = {The structure of {DNA} in a nucleosome},
  journal = PNAS,
  year = {1990},
  volume = {88},
  pages = {6829--6833},
  annote = {gives the helix repeat as 10.7 at dyad and 10.0 elsewhere in nucleosome}
}

@ARTICLE{VONH90,
  author = {G. von Heijne and C. Manoil},
  title = {Membrane proteins: from sequence to structure},
  journal = {Protein Engineering },
  year = {1990},
  volume = {4},
  pages = {109}
}

@ARTICLE{HELF90,
  author = {Helfrich, P. and E. Jakobsson},
  title = {Calculation of deformation energies and conformations in lipid membranes
	containing gramicidin channels},
  journal = {Biophys. J.},
  year = {1990},
  volume = {57},
  pages = {1075--1084},
  annote = {requested Tx=19920924.}
}

@ARTICLE{HeGS90,
  author = {H. Heller and H. Grubm{\"u}ller and K. Schulten},
  title = {Molecular Dynamics Simulation on a Parallel Computer},
  journal = {Molecular Simulation},
  year = {1990},
  volume = {5},
  pages = {133--165}
}

@ARTICLE{HELL90,
  author = {Helmut Heller and Helmut Grubm{\"u}ller and Klaus Schulten},
  title = {Molecular Dynamics Simulation on a Parallel Computer},
  journal = MS,
  year = {1990},
  volume = {5},
  pages = {133--165}
}

@ARTICLE{HEND90,
  author = {R. Henderson and J. M. Baldwin and T. A. Ceska and F. Zemlin and
	E. Beckmann and K. H. Downing},
  title = {Model for the Structure of Bacteriorhodopsin Based on High-Resolution
	Electron Cryo-microscopy},
  journal = JMB,
  year = {1990},
  volume = {213},
  pages = {899--929}
}

@ARTICLE{HO90,
  author = {Chris M. W. Ho and Garland Marshall},
  title = {Cavity search: An algorithm for the isolation and display of cavity-like
	binding-regions},
  journal = JCAMD,
  year = {1990},
  volume = {4},
  pages = {337--354},
  annote = {GM is an editor of this journal; gives overview of many different
	approaches used so far; describes his program to produce a cast of
	the binding site; by means of a seed point the cavity of interest
	can be selected; the whole approach seems to be very idiosyncratic
	and it seems to me he just tries to cope with deficiencies of SYBYL,
	very detailed description; the idea itself is quite interesting and
	seems useful},
  keywords = {cavity search; ligand-receptor interaction; molecular graphics; solid
	modeling, HIV-1; MVT-101}
}

@ARTICLE{HOLM90,
  author = {Kenneth C. Holmes and David Popp and Werner Gebhard and Wolfgang
	Kabsch},
  title = {Atomic model of the actin filament},
  journal = NAT,
  year = {1990},
  volume = {347},
  pages = {44--49}
}

@ARTICLE{HUDS90,
  author = {J. Michael Hudson and Michael G. Fried},
  title = {Co-operative interactions between the catabolite gene activator protein
	and the {\it lac} repressor at the lactose promoter},
  journal = JMB,
  year = {1990},
  volume = {214},
  pages = {381--396}
}

@ARTICLE{HUNT90,
  author = {N. Hunter and H. Bergstrom and R. {van Grondelle} and V. Sundstrom},
  title = {Energy-Transfer Dynamics in Three Light-Harvesting Mutants of {\em
	{R}hodobacter sphaeroides}: A picsecond spectroscopy study},
  journal = {Biochem.~},
  year = {1990},
  volume = {29},
  pages = {3203--3207}
}

@BOOK{HYNE90,
  title = {Fibronectins},
  publisher = {Springer-Verlag},
  year = {1990},
  author = {R.O. Hynes},
  address = {New York}
}

@INPROCEEDINGS{HYSL90,
  author = {W. Brian Hyslop and Paul C. Lauterbur},
  title = {Effects of Restricted Diffusion in {NMR} Microscopy},
  booktitle = {Book of Abstracts},
  year = {1990},
  volume = {1},
  pages = {393},
  organization = smrm,
  brief = {motional narrowing, edge enhancement}
}

@ARTICLE{HARD90b,
  author = {T.~H{\"a}rd and K.~Dahlman and J.~C.~Duke and J.~Gustafsson and R.~Rigler},
  title = {Cooperativity and specificity in the interactions between {DNA} and
	the glucocorticoid receptor {DNA}--binding domain},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {5358--5364},
  annote = {says that DBD of GR bind highly cooperatively to half-sites separated
	by 3bp, works with SCHW90 for ER and HARD90}
}

@ARTICLE{HARD90,
  author = {T.~ H{\"a}rd and E.~Kellenbach and R.~Boelens and B.~A.~Maler and
	K.~Dahlman and L.~P.~Freedman and J.~Carlstedt-Duke and K.~R.~Yamamoto
	and J.~Gustafsson and R.~Kaptein},
  title = {Solution Structure of the Glucocorticoid Receptor {\sc DNA}--Binding
	Domain},
  journal = SCI,
  year = {1990},
  volume = {249},
  pages = {157--160},
  annote = {71 residue protein fragement, DBD, fingers, Xenopus TFIIIa isolated
	DBD GR are monomeric in solution see also Schw90,and HARD90b}
}

@ARTICLE{IPSE90,
  author = {J.H. Ipsen and K. J{\"o}rgensen and O.G. Mouritsen},
  title = {Density fluctuations in saturated phospholipid bilayer increase as
	the acyl-chain length decreases},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {1099--1107}
}

@TECHREPORT{Iser90,
  author = {A. Iserles},
  title = {Efficient \mbox{Runge-Kutta} Methods for {H}amiltonian Equations},
  institution = {Dept. of Appl. Math. and Theoretical Phys.,},
  year = {1990},
  number = {DAMMTP 1990/NA10},
  address = {Univ. of Cambridge, England}
}

@ARTICLE{ISRA90,
  author = {Jacob N. Israelachvili and H{\aa}kan Wennerstr{\"o}m},
  title = {Hydration or Steric forces between Amphiphilic Surfaces?},
  journal = LM,
  year = {1990},
  volume = {6},
  pages = {873--876},
  annote = {strong repulsive short range force, so-called hydration force, is
	*not* due to water structure but results from entropic repulsion
	of molecular groups that are thermally excited and protrude from
	the surfce; overview-like: integrations available data; out-of-plane
	motion of single lipid molecules; phone: (805)893-8407},
  keywords = {surface; theory; hydration/structural/solvation forces; undulation;
	pertrusion; entropic confinement; pressure; head groups},
  suggestions = {look at surface roughness (lipid-CM movement and head group movement)
	of gel phase and compare with fluid phase}
}

@ARTICLE{JANM90,
  author = {Paul A. Janmey and Soren Hvidt and George F. Oster and Jennifer Lamb
	and Thomas P. Stossel and John H. Hartwig},
  title = {Effect of {ATP} on actin filament stiffness},
  journal = NAT,
  year = {1990},
  volume = {347},
  pages = {95--99}
}

@ARTICLE{JANT90,
  author = {H.-M. Jantzen and A. Admon and S. P. Bell and R. Tjian},
  title = {Nucleolar transcription factor {hUBF} contains a {DNA}-binding motif
	with homology to {HMG} proteins},
  journal = NAT,
  year = {1990},
  volume = {344},
  pages = {830--836}
}

@ARTICLE{JONA90,
  author = {A. Jonas and J. Hefele Wald and K. L. Harms Toohill and E. S. Krul
	and K. E. Kezdy},
  title = {Apolipoprotein {A-I} Structure and Lipid Properties in Homogeneous
	Reconstituted Spherical and Discoidal High Density Lipoproteins},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {22123--22129}
}

@ARTICLE{JAEH90,
  author = {Fritz J{\"a}hnig and Olle Edholm},
  title = {Can the Structure of Proteins be Calculated?},
  journal = ZPB,
  year = {1990},
  volume = {78},
  pages = {137--143},
  annote = {structure prediction for bR; partial unfolding of F helix observed},
  keywords = {bR, membrane}
}

@ARTICLE{KABS90,
  author = {W. Kabsch and H.~G. Mannherz and D. Suck and E.~F. Pai and K.C. Holmes},
  title = {Atomic Structure of the Actin:{DN}ase {I} Complex},
  journal = NAT,
  year = {1990},
  volume = {347},
  pages = {37--44}
}

@BOOK{KALL90,
  title = {Chemistry \& Physics of {DNA}-Ligand Interactions},
  publisher = {Adenine Press},
  year = {1990},
  author = {N. R. Kallenbach},
  address = {2066 Central Avenue, Schenectady, NY}
}

@INPROCEEDINGS{KALE90,
  author = {L. V. Kal{\'e}},
  title = {The Chare Kernel Parallel Programming Language and System},
  booktitle = {Proc.\ of the International Conf.\ on Parallel Processing},
  year = {1990},
  volume = {2},
  pages = {17--25}
}

@ARTICLE{KARN90,
  author = {Sadashiva Karnik and Tomolo Doi and R. Molday and H. Gobind Khorana},
  title = {Expression of the Archaebacterial Bacterio-opsin Gene with and without
	Signal Sequeneces in {\it {E}scheria coli}: {T}he Expressed Proteins
	are Located in the Membrane but Bind Retinal Poorly},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {8955--8959}
}

@INPROCEEDINGS{KARP90,
  author = {Martin Karplus},
  title = {Molecular Dynamics: Applications to Proteins},
  booktitle = {Modelling of Molecular Structures and Properties},
  year = {1990},
  editor = {J.-L. Rivail},
  volume = {71},
  series = {Studies in Physical and Theoretical Chemistry},
  pages = {427--461},
  address = {Amsterdam},
  publisher = {Elsevier Science Publishers},
  note = {Proceedings of an International Meeting},
  annote = {General paper. Good introduction. Historical facts. Overview/review.
	Many applications of MD are described. Many references.},
  keywords = {myoglobin, temperature factors, refinement}
}

@ARTICLE{KARP90a,
  author = {M. Karplus and Gregory A. Petsko},
  title = {Structure model of a complex between the {Factor for Inversion Stimulation
	(FIS)} and {DNA}: {Modeling} protein-{DNA} complexes with dyad symmetry
	and known protein structures},
  journal = NAT,
  year = {1990},
  volume = {347},
  pages = {631--639}
}

@ARTICLE{KAUL90,
  author = {A. D. Kaulen and N. V. Postanogova},
  title = {{pH} Dependence of the Dark Equilibrium Between 13-{\it cis}- and
	{\it trans}-Bacteriorhodopsins of Purple Membranes},
  journal = UNKNOWN,
  year = {1990},
  volume = UNKNOWN,
  pages = {516--519}
}

@ARTICLE{KESZ90,
  author = {L. Keszthelyi and S. Sz{\'a}raz and A. D{\'e}r adn W. Stoechenius},
  title = {Bacteriorhodopsin and Halorhodopsin: Multiple Ion Pumps},
  journal = BBA,
  year = {1990},
  volume = {1018},
  pages = {260--262}
}

@ARTICLE{KIM90,
  author = {P. S. Kim and R. L. Baldwin},
  title = {Intermediates in the Folding Reactions of Small Proteins},
  journal = {Ann.\ Rev.\ Biochem.},
  year = {1990},
  volume = {59},
  pages = {631--660}
}

@ARTICLE{KNEL90,
  author = {D. G. Kneller and F. E. Cohen and R. Langridge},
  title = {Improvements in Protein Secondary Structure Prediction by an Enhanced
	Neural Network},
  journal = JMB,
  year = {1990},
  volume = {214},
  pages = {171--182}
}

@ARTICLE{KOBA90,
  author = {T. Kobayashi and M. Terauchi and T. Kouyama and M. Yoshizawa and
	M. Taiji},
  title = {Femtosecond Spectroscopy of Acidified and Neutral Bacteriorhodopsin},
  journal = SPIE,
  year = {1990},
  volume = {1403},
  pages = {407--416}
}

@ARTICLE{KOLL90,
  author = {P.A. Kollman and K.M. {Merz Jr.}},
  title = {Computer modeling of the interactions of complex molecules},
  journal = {Acc. Chem. Res.},
  year = {1990},
  volume = {23},
  pages = {246--252}
}

@ARTICLE{KotC90,
  author = {J.~Kottalam and D.~A.~Case},
  title = {Langevin modes of macromolecules: applications to crambin and {DNA}
	hexamers},
  journal = BP,
  year = {1990},
  volume = {29},
  pages = {1409--1421},
  number = {10--11}
}

@ARTICLE{KUIP90,
  author = {O.P. Kuipers and P.A. Franken and R. Hendriks and H.M. Verheij and
	G.H. de Haas},
  title = {Function of the fully conserved residues {A}sp99, {T}yr52 and {T}yr
	73 in phospholipase {A$_2$}},
  journal = {Protein Engineering},
  year = {1990},
  volume = {4},
  pages = {199--204}
}

@ARTICLE{KuHi90a,
  author = {T. Kuusela and J. Hietarinta},
  title = {Numerical, Experimental, and Analytical Studies of the Dissipative
	Toda Lattice \mbox{I. } \mbox{T}he Behavior of a Single Solitary
	Wave},
  journal = {Physica D},
  year = {1990},
  volume = {41},
  pages = {322--340}
}

@ARTICLE{KuHi90b,
  author = {T. Kuusela and J. Hietarinta},
  title = {Numerical, Experimental, and Analytical Studies of the Dissipative
	{T}oda Lattice \mbox{II}},
  journal = {Physica D},
  year = {1990},
  volume = {46},
  pages = {1--9}
}

@ARTICLE{LAFL90,
  author = {M. Lafleur and P. R. Cullis and M. Bloom},
  title = {Modulation of the orientational order profile of the lipid acyl chain
	in the {$L_{\alpha}$} phase},
  journal = EBJ,
  year = {1990},
  volume = {19},
  pages = {55--62},
  annote = {POPC is in $L_{\alpha}$ phase (liquid crystalline) from $0^o$\,C
	to $70^o$\,C; POPC representative for lipid combination found in
	in eucaryotic cells (those with a nucleus); POPC phase transition
	from gel to liquid at $-6^o$\,C; experimental order parameter profiles:
	S(n) around 0.1 to 0.25; concept of reduced temperature challenged;
	plateau region typical for L_\alpha (LC) phase; lateral pressure
	might be the crucial parameter influencing the order parameters},
  keywords = {POPC; membrane; experimental; orientational order; $^2$H-NMR; phospholipid;
	hydrocarbon chain; POPE; cholesterol; order parameter; phase transition;
	lipid-protein interaction},
  suggestions = {look at mean and width of order parameter distribution}
}

@ARTICLE{LEAR90,
  author = {James D. Lear},
  title = {Why Did the Voltage Sensor Cross the Membrane?},
  journal = CTB,
  year = {1990},
  volume = {1},
  pages = {329--340},
  number = {6}
}

@BOOK{LERN90,
  title = {Encyclopedia of Physics},
  publisher = {VCH Publisher, Inc.},
  year = {1990},
  author = {Rita G. Lerner and George L. Trigg},
  address = {New York},
  edition = {2}
}

@ARTICLE{LEVI90,
  author = {R. D. Levine},
  title = {The Chemical Shape of Molecules: An Introduction to Dynamical Stereochemistry},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {8872--8880},
  annote = {many (93) references; overview article; very chemical, hard to read,
	not interesting},
  keywords = {physical shape; chemical shape; reactivity; chemical reactions}
}

@ARTICLE{LI90,
  author = {J. Li and A. Brass and D.~J. Ward and B. Robson},
  title = {A Study of Parallel Molecular Dynamics Algorithms for $N$-Body Simulations
	on a Transputer System},
  journal = PA,
  year = {1990},
  volume = {14},
  pages = {211--222},
  annote = {not a very interesting article}
}

@ARTICLE{LONC90,
  author = {Richard J. Loncharich and Bernard R. Brooks},
  title = {Temperature Dependence of Dynamics of Hydrated Myoglobin},
  journal = JMB,
  year = {1990},
  volume = {215},
  pages = {439--455},
  annote = {dihedral transitions; Richard J. Loncharich works now for Ely Lilly
	and we cooperate with him},
  keywords = {neutron scatering; molecular dynamics}
}

@INCOLLECTION{NIES90,
  author = {R. L. Magin and M. R. Niesman and G. Bacic},
  title = {The Influence of Fluidity on Membrane Permeability: Correspondence
	Between Studies of Membrane Models and Simple Biological Systems},
  booktitle = {Advances in Membrane Fluidity, Band 4},
  publisher = {A.~R.~Liss},
  year = {1990},
  editor = {R. C. Aloia and C. C. Curtain and L. M. Gorden},
  address = {New York},
  keywords = {liposomes}
}

@ARTICLE{MAK90,
  author = {C. H. Mak and David Chandler},
  title = {Solving the Sign Problem in Quantum {M}onte {C}arlo Dynamics},
  journal = PRA,
  year = {1990},
  volume = {41},
  pages = {5709--5712}
}

@ARTICLE{MART90,
  author = {Thomas Martinetz and Helge Ritter and Klaus Schulten},
  title = {Three-Dimensional Neural Net for Learning Visuo-Motor Coordination
	of a Robot Arm},
  journal = IEEENN,
  year = {1990},
  volume = {1},
  pages = {131--136}
}

@INCOLLECTION{MART90A,
  author = {Thomas Martinetz and Helge Ritter and Klaus Schulten},
  title = {Learning of Visuo Motor-Coordination of a Robot Arm with Redundant
	Degrees of Freedom},
  booktitle = {Parallel Processing in Neural Systems and Computers},
  publisher = {Elsevier},
  year = {1990},
  editor = {R. Eckmiller and G. Hartmann and G. Hauske},
  pages = {431--434},
  address = {Amsterdam},
  annote = {This book is contains the proceedings of the Int. Conf. on Parallel
	Processing in Neural Systems and Computers {(ICNC)}, D\"usseldorf,
	March 1990}
}

@INCOLLECTION{MART90B,
  author = {Thomas Martinetz and Klaus Schulten},
  title = {Hierarchical Neural Net for Learning Control of a Robot's Arm and
	Gripper},
  booktitle = {International Joint Conference on Neural Networks, San Diego, California},
  publisher = {The Institute of Electrical and Electronics Engineers},
  year = {1990},
  volume = {2},
  pages = {747--752},
  address = {New York}
}

@ARTICLE{MCDO90,
  author = {H.B. McDonald and L.S.B. Goldstein},
  title = {Identification and characterization of a gene encoding a kinesin-like
	protein in {{\em Drosophila}}},
  journal = CEL,
  year = {1990},
  volume = {61},
  pages = {991--1000}
}

@ARTICLE{MCDO90A,
  author = {H.B. McDonald and R.J. Stewart and L.S.B. Goldstein},
  title = {The kinesin-like ncd protein of {{\em Drosophila}} is a minus-end
	directed microtubule motor},
  journal = CEL,
  year = {1990},
  volume = {63},
  pages = {1159--1165}
}

@ARTICLE{MCIN90,
  author = {L.\ P.\ McIntosh and A.\ J.\ Wand and D.\ F.\ Lowry and A.\ G.\ Redfield
	and F.\ W.\ Dahlquist},
  title = {Assignment of the Backbone {H}-1 and {N}-15 {NMR} Resonances of Bacteriophage-{T}4
	Lysozyme},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {6341--6362}
}

@ARTICLE{MILB90,
  author = {M. V. Milburn and L. Tong and A. M. {de\,Vos} and A. Brunger and
	Z. Yamaizumi and S. Nishimura and S.-H. Kim},
  title = {Molecular switch for signal transduction: structural differences
	between active and inactive forms of protooncogenic ras proteins},
  journal = SCI,
  year = {1990},
  volume = {247},
  pages = {939--945}
}

@INCOLLECTION{MILL90,
  author = {K.~D. Miller},
  title = {Correlation based models of neural development},
  booktitle = {Neuroscience and Connectionst Theory},
  publisher = {Lawrence Erlbaum Associates},
  year = {1990},
  editor = {M.~Gluck and D.~Rumelhart},
  pages = {267--354}
}

@ARTICLE{MILL90A,
  author = {R. A. Milligan and M. Whittaker and D. Safer},
  title = {Molecular structure of {F}-actin and location of surface binding
	sites},
  journal = NAT,
  year = {1990},
  volume = {348},
  pages = {217--221}
}

@ARTICLE{MOE90,
  author = {J.~G.~Moe and I.~M.~Russu.},
  title = {Proton exchange and base-pair opening kinetics in 5'-d{(CGCGAATTCGCG)}-3'
	and related dodecamers},
  journal = NAR,
  year = {1990},
  volume = {18},
  pages = {821--827}
}

@INPROCEEDINGS{MOUR90,
  author = {O.G. Mouritsen},
  title = {Computer simulation of cooperative phenomela in lipid membranes},
  booktitle = {Molecular description of biological membrane components by computer
	aided conformational analysis, Vol.1},
  year = {1990},
  editor = {R. Brasseur},
  pages = {3--83},
  address = {Boca Raton, Florida},
  journal = {CRC press}
}

@ARTICLE{MULL90A,
  author = {N. Muller},
  title = {Search for a Realistic View of Hydrophobic Effects},
  journal = ACR,
  year = {1990},
  volume = {23},
  pages = {23--28}
}

@BOOK{MULL90,
  title = {Neural Networks, An Introduction},
  publisher = {Spinger-Verlag},
  year = {1990},
  author = {B. M{\"u}ller and J. Reinhardt},
  address = {Berlin Herdelberg}
}

@ARTICLE{NAGA90,
  author = {V. Nagarajan and W. W. Parson and D. Gaul and C. Schenck},
  title = {Effect of Specific Mutations of Tyrosine-(M)210 on the Primary Photosynthetic
	Electron-Transfer Process in Rhodobacter Sphaeroides},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {7888--7892}
}

@ARTICLE{NELS90,
  author = {M. E. Nelson and J. M. Bower},
  title = {Brain Maps and Parallel Computers},
  journal = TINS,
  year = {1990},
  volume = {13},
  pages = {401--406}
}

@ARTICLE{NeCo90,
  author = {S. A. Newman and W. Comper},
  title = {Generic Physical Mechanisms of Morphogenesis and Pattern Formation},
  journal = {Development},
  year = {1990},
  volume = {110},
  pages = {1--18}
}

@ARTICLE{NI90,
  author = {B. Ni and M. Chang and A. Duschl and J. Lanyi and R. Needleman},
  title = {An Efficient System for the Synthesis of Bacteriorhodopsin in {{\em
	Halobacterium halobium}}},
  journal = {Gene},
  year = {1990},
  volume = {90},
  pages = {169--172}
}

@ARTICLE{NOGU90,
  author = {T. Noguchi and S. Kolaczkowski and W. G{\"a}rtner and G. H. Atkinson},
  title = {Resonance Raman Spectra of 13-Demethylretinal Bacteriorhodopsin and
	of a Picosecond Bathochromic Photocycle Intermediate},
  journal = JPC,
  year = {1990},
  volume = {94},
  pages = {4920--4926}
}

@INPROCEEDINGS{OBER90B,
  author = {Klaus Obermayer and Helmut Heller and Helge Ritter and Klaus Schulten},
  title = {Simulation of Self-Organizing Neural Nets: A Comparision Between
	a Transputer Ring and a {C}onnection {M}achine {CM-2}},
  booktitle = {{NATUG~3}: Transputer Research and Applications~3},
  year = {1990},
  editor = {Alan S. Wagner},
  pages = {95--106},
  address = {Amsterdam},
  organization = {North American Transputer Users Group},
  publisher = {{IOS} Press},
  annotes = {Proceedings of the Third Conference of the North American Transputer
	Users Group, April~26--27, 1990 --- Sunnyvale, CA}
}

@INCOLLECTION{OBER90,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {Large-Scale Simulation of a Self-Organizing Neural Network: Formation
	of a Somatotopic Map},
  booktitle = {Parallel Processing in Neural Systems and Computers},
  publisher = {Elsevier},
  year = {1990},
  editor = {R. Eckmiller and G. Hartmann and G. Hauske},
  pages = {71--74},
  address = {Amsterdam},
  annote = {This book is contains the proceedings of the Int. Conf. on Parallel
	Processing in Neural Systems and Computers {(ICNC)}, D\"usseldorf,
	March 1990}
}

@ARTICLE{OBER90A,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {A Principle for the Formation of the Spatial Structure of Cortical
	Feature Maps},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {8345--8349}
}

@INCOLLECTION{OBER90C,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {A Neural Network Model for the Formation of Topographic Maps in the
	{CNS}: Development of Receptive Fields},
  booktitle = {International Joint Conference on Neural Networks, San Diego, California},
  publisher = {The Institute of Electrical and Electronics Engineers},
  year = {1990},
  volume = {2},
  pages = {423--429},
  address = {New York}
}

@ARTICLE{OBER90D,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {Large-Scale Simulations of Self-Organizing Neural Networks on Parallel
	Computers: Application to Biological Modelling},
  journal = PA,
  year = {1990},
  volume = {14},
  pages = {381--404}
}

@ARTICLE{RITT90A,
  author = {Klaus Obermayer and Helge Ritter and Klaus Schulten},
  title = {Large-Scale Simulations of Self-Organizing Neural Networks on Parallel
	Computers: Application to Biological Modelling},
  journal = PA,
  year = {1990},
  volume = {14},
  pages = {381--404}
}

@ARTICLE{OEHL90,
  author = {Stephan Oehler and Elisabeth R. Eismann and and Helmut Kr{\"a}mer
	and Benno M{\"u}ller-Hill},
  title = {The three operators of the {\it lac} operon cooperate in repression},
  journal = EMBO,
  year = {1990},
  volume = {9},
  pages = {973--979},
  number = {4}
}

@ARTICLE{YUKO90,
  author = {Yuko Ohara-Nemoto and Per-Erik Str\"omtedt and Karin Dahlman-Wright
	and Takayuki Nemoto and J.~Gustafsson and Jan Carlstedt-Duke},
  title = {The Steroid-Binding Properties of Recombinant Glucocorticoid Receptor:
	A Putative Role for Heat Shock Protein hsp90},
  journal = {J.\ Steroid Biochem.\ Molec.\ Biol.},
  year = {1990},
  volume = {37},
  pages = {481--490},
  annote = {role of hormone in the cell, function of GR}
}

@ARTICLE{OTTO90,
  author = {Otto, H. and Marti, T. and Holz, M. and Mogi, T. and Stern, L. J.
	and Engel, F. and Khorana, H. G. and Heyn, M. P.},
  title = {Substitution of amino acids {Asp-85}, {Asp-212}, and {Arg-82} in
	bacteriorhodopsin affects the proton release phase of the pump and
	the {pK} of the {Schiff} base},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {1018--1022}
}

@INPROCEEDINGS{tcl,
  author = {John K. Ousterhout},
  title = {Tcl: An Embeddable Command Language},
  booktitle = {1990 Winter {USENIX} Conference Proceedings},
  year = {1990},
  organization = {{USENIX}},
  note = {ftp://ftp.scriptics.com/pub/tcl/doc/tclUsenix90.ps}
}

@ARTICLE{PACK90,
  author = {M. J. Packer and W. T. Raynes},
  title = {Electric field effects on the $^{13}$C and $^{19}$F nuclear shielding
	in HF and CH$_3$F},
  journal = MP,
  year = {1990},
  volume = {69},
  pages = {391--400}
}

@ARTICLE{PAIN90,
  author = {G. R. Painter and J. P. Shockcor and C. W. Andrews},
  title = {Application of molecular mechanics to the study of drug-membrane
	interactions},
  journal = {Advances in molecular modeling},
  year = {1990},
  volume = {2},
  pages = {135--163},
  annote = {The role of conformation in the passive membrane permeability of
	zidovudine}
}

@ARTICLE{PAPA90,
  author = {G. Papadopoulos and N. Dencher and G. Zacca{\"{\i}} and G. B{\"u}ldt},
  title = {Water Molecules and Exchangeable Hydrogen Ions at the Active Centre
	of Bacteriorhodopsin Localized by Neutron Diffraction},
  journal = {J. Mol. Biol.},
  year = {1990},
  volume = {214},
  pages = {15--19}
}

@INCOLLECTION{PARK90,
  author = {T. P. Parks and S. Lukas and A. F. Hoffman},
  title = {Purification and characterization of a Phospholipase {A}$_2$ from
	Human Osteoarthritic Synovial fluid},
  booktitle = {Phospholipase {A}$_2$},
  publisher = {Plenum Press},
  year = {1990},
  editor = {P. Y. K. Wong and E. A. Dennis},
  pages = {55--80},
  address = {New York}
}

@ARTICLE{PAST90,
  author = {Annalisa Pastore and Vladimir Saudek},
  title = {The Relationship between Chemical Shift and Secondary Structure in
	Proteins},
  journal = {J.\ Magnetic Resonance},
  year = {1990},
  volume = {90},
  pages = {165--176}
}

@ARTICLE{PECK90,
  author = {Tim Peck and Richard Magin and Paul Lauterbur},
  title = {Microdomain Magnetic Resonance Imaging},
  journal = {Abstracts, 9th Annual Meeting SMRM},
  year = {1990},
  pages = {270},
  address = {New York}
}

@TECHREPORT{PeAs90,
  author = {L. R. Petzold and U. Ascher},
  title = {Projected implicit {R}unge-{K}utta methods for differential-algebraic
	equations},
  institution = {Lawrence Livermore National Laboratory, California},
  year = {1990},
  number = {Rpt.\ No.\ UCRL-JC-104037}
}

@ARTICLE{PINA90,
  author = {B.~Pi{\~n}a and U.~Br{\"u}ggemeier and M.~Beato},
  title = {Nucleosome Positioning Modulates Accessibility of Regulatory Proteins
	to the Mouse Mammary Tumor Virus Promoter},
  journal = {Cell},
  year = {1990},
  volume = {60},
  pages = {719--731},
  annote = {cross ref to WOFL94}
}

@ARTICLE{POLL90,
  author = {W. T. Pollard and S. Y. Lee and R. A. Mathies},
  title = {Wave Packet Theory of Dynamics Absorption Spectra in Femtosecond
	Pump-Probe Experiments},
  journal = JCP,
  year = {1990},
  volume = {92},
  pages = {4012--4029}
}

@ARTICLE{POPO90,
  author = {J.L. Popot and D.M. Engelman},
  title = {Membrane protein folding and oligomerization: the two-stage model},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {4031--4037}
}

@ARTICLE{POPO90a,
  author = {J. Popot and C. de Vitry},
  title = {On the microassembly of integral membrane proteins},
  journal = {Annual Review of Biophysics and Biophysical Chemistry},
  year = {1990},
  volume = {19},
  pages = {369}
}

@ARTICLE{POUN90,
  author = {Dick Pountain},
  title = {Virtual Channels: The Next Generation of {T}ransputers},
  journal = {Byte},
  year = {1990},
  pages = {E\&W~3--12}
}

@ARTICLE{QiZh90a,
  author = {M.-Z. Qin and M.-Q. Zhang},
  title = {Explicit \mbox{Runge-Kutta-like} Schemes to Solve Certain Quantum
	Operator Equations of Motion},
  journal = {J. Stat. Phys.},
  year = {1990},
  volume = {60},
  pages = {839--843},
  number = {5/6}
}

@ARTICLE{QiZh90b,
  author = {M.-Z. Qin and M.-Q. Zhang},
  title = {Multi-stage symplectic schemes of two kinds of {H}amiltonian systems
	for wave equation},
  journal = {Computers Math.\ with\ Applic.},
  year = {1990},
  volume = {19},
  pages = {51--62}
}

@ARTICLE{QuTr90,
  author = {G. D. Quinlan and S. Tremaine},
  title = {Symmetric multistep methods for the numerical integration of planetary
	orbits},
  journal = {Astron. J.},
  year = {1990},
  volume = {100},
  pages = {1694--1700}
}

@INPROCEEDINGS{RAIN90,
  author = {A. R. C. Raine},
  title = {Molecular Dynamics Simulation of Proteins on an Array of Transputers},
  booktitle = {Applications of Transputers~2., Proccedings of the Second International
	Conference on Applications of Transputers},
  year = {1990},
  editor = {Pritchard, D.~J. and Scott, C. J.},
  pages = {272--279},
  address = {Amsterdam, Netherlands},
  publisher = {{IOS} Press},
  annote = {Conference Date: 11--13 July 1990, Southampton, UK},
  keywords = {parallel SHAKE; SLS; 3 and 4 body interactions; GROMOS},
  other = {INSPEC Abstract Number: A90149581, C90072511}
}

@BOOK{RITT90,
  title = {{Textbook: Neuronale Netze: Eine Einf\"uhrung in die Neuroinformatik
	selbstorganisierender Abbildungen}},
  publisher = {Ad\-di\-son-Wesley},
  year = {1990},
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  address = {Bonn},
  edition = {2nd}
}

@BOOK{RITT90C,
  title = {Textbook: Neuronale Netze: Eine Einf\"uhrung in die Neuroinformatik
	selbstorganisierender Abbildungen},
  publisher = {Ad\-di\-son-Wesley},
  year = {1990},
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  address = {Bonn},
  edition = {First}
}

@ARTICLE{ROJE90,
  author = {A. S. Rojer and E. L. Schwartz},
  title = {Cat and Monkey Cortical Columnar Patterns Modeled by Bandpass-Filtered
	2D White Noise},
  journal = BC,
  year = {1990},
  volume = {62},
  pages = {381--391}
}

@ARTICLE{ROTH90,
  author = {K. J. Rothschild and M. S. Braiman and Y. W. He},
  title = {Vibrational Spectroscopy of Bacteriorhodopsin Mutants. Evidence for
	the Interaction of Aspartic Acid 212 with Tyrosine 185 and Possible
	Role in the Proton Pump Mechanism.},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {16985--16991}
}

@ARTICLE{RUBN90,
  author = {Jeanne Rubner and Klaus Schulten},
  title = {Development of Feature Detectors by Self-Organization: A Network
	Model},
  journal = BC,
  year = {1990},
  volume = {62},
  pages = {193--199}
}

@INCOLLECTION{RUBN90A,
  author = {Jeanne Rubner and Klaus Schulten and Paul Tavan},
  title = {A Self-Organizing Network for Complete Feature Extraction},
  booktitle = {Parallel Processing in Neural Systems and Computers},
  publisher = {Elsevier},
  year = {1990},
  editor = {R. Eckmiller and G. Hartmann and G. Hauske},
  pages = {365--368},
  address = {Amsterdam},
  annote = {This book is contains the proceedings of the Int. Conf. on Parallel
	Processing in Neural Systems and Computers {(ICNC)}, D\"usseldorf,
	March 1990}
}

@ARTICLE{SANT90A,
  author = {B. D. Santarsiero and M. N. G. James},
  title = {Crystal Structure of {\it N}-Methyl-{\it N}-phenylretinal Iminium
	Perchlorate: A Structural Model for the Bacteriorhodopsin Chromophore},
  journal = JACS,
  year = {1990},
  volume = {112},
  pages = {9416--9418}
}

@ARTICLE{SANT90,
  author = {G. E. Santyr and I. Kay and R. M. Henkelman and M. J. Bronskill},
  title = {Diffusive Exchange Anaylsis of Two-Component T$_2$ Relaxation of
	Red Blood Cell Suspensions Containing Gadolinium},
  journal = {J.\ Magnetic Resonance},
  year = {1990},
  volume = {90},
  pages = {500--513},
  brief = {Uses finite different approx. to get bi-exp decay for T2 realxation
	due to exchange across cell membranes},
  keywords = {Gd-DTPA}
}

@ARTICLE{SASA90,
  author = {M. Sasai and P. G. Wolynes},
  title = {Molecular Theory of Associative Memory {Hamiltonian} Models of Protein
	Folding},
  journal = {Phys. Rev. Lett.},
  year = {1990},
  volume = {65},
  pages = {2740}
}

@ARTICLE{SHWS90,
  author = {Martin Saunders and K. N. Houk and Yun-Dong Wu and W. Clark Still
	and Mark Lipton and George Chang and Wayne C. Guida},
  title = {Conformations of Cycloheptadecan. A Comparison of Methods for Conformational
	Searching},
  journal = ACS,
  year = {1990},
  volume = {112},
  pages = {1419--1427}
}

@ARTICLE{SAWA90,
  author = {J. Sawatzki and R. Fischer and H. Scheer and F. Siebert},
  title = {Fourier-transform Raman spectroscopy applied to photobiological systems.},
  journal = BIO,
  year = {1990},
  volume = {87},
  pages = {5903--5906}
}

@ARTICLE{SCHA90,
  author = {Michael Schaefer and Cornelius Froemmel},
  title = {A Precise Analytical Method for Calculating the Electrostatic Energy
	of Macromolecules in Aqueous Solution},
  journal = JMB,
  year = {1990},
  volume = {216},
  pages = {1045--1066}
}

@INPROCEEDINGS{SCHL90,
  author = {M. Schlenkrich and K. Nicklas and J. B{\"o}cker and P. Bopp and J.
	Brinckmann},
  title = {Structure and Dynamics of Water and Ionic Solutions Near Biomolecular
	Surfaces From Molecular Dynamics Simulations},
  booktitle = {Modelling of Molecular Structures and Properties},
  year = {1990},
  editor = {J.-L. Rivail},
  volume = {71},
  series = {Studies in Physical and Theoretical Chemistry},
  pages = {245--252},
  address = {Amsterdam},
  publisher = {Elsevier Science Publishers},
  note = {Proceedings of an International Meeting},
  annote = {simple charged membrane model; layering of water; 737 TIP4P water
	molecules; 60 COO^- groups represent the membrane; water density
	increases close to the membrane; water is immobilized near membrane},
  keywords = {simulation},
  suggestions = {distribution functions (density profiles) of water oxygenl velocity
	autocorrelation function}
}

@ARTICLE{SCHN90,
  author = {B.J. Schnapp and C. Crise and M.P. Sheetz and T.S. Reese and S. Khan},
  title = {Delayed start-up of kinesin-driven microtubule gliding following
	inhibition by adenosine 5'-[$\beta$,$\gamma$-imido]triphosphate},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {10053--10057}
}

@ARTICLE{SCHR90,
  author = {R.~Schreck and H.~Zorbas and E.~L.~Winnacker and P.~A.~Baeuerle},
  title = {The NF-kB transcription factor induces {DNA} bending which is modulated
	by its 65-k{\sc D} subunit.},
  journal = {Nucleic Acids Research},
  year = {1990},
  volume = {18},
  pages = {6497--6502},
  annote = {not read, eukaryotic sytems}
}

@ARTICLE{SCHW90,
  author = {J.~W.~R.~Schwabe and David Neuhaus and Daniela Rhodes},
  title = {Solution structure of the {DNA}--binding domain of the oestrogen
	receptor.},
  journal = NAT,
  year = {1990},
  volume = {348},
  pages = {458--461},
  annote = {it displays that ER is in agreement with GR for the DBD.}
}

@ARTICLE{SCOT90,
  author = {D. L. Scott and S. P. White and Z. Otwinowski and W. Yuan and M.
	H. Gelb and P. B. Sigler},
  title = {Interfacial Catalysis: The Mechanism of Phospholipase~{A}$_2$},
  journal = SCI,
  year = {1990},
  volume = {250},
  pages = {1541--1546}
}

@ARTICLE{SCOT90a,
  author = {David L. Scott and Steven P. White and Zbyszek Otwinowski and Wei
	Yuan and Michael H. Gelb and Paul B. Sigler},
  title = {Interfacial Catalysis: The Mechanism of Phospholipase A2},
  journal = SCI,
  year = {1990},
  volume = {250},
  pages = {1541--1546}
}

@ARTICLE{SEMM90,
  author = {P. Semm and R. C. Beason},
  title = {Sensory basis of bird orientation},
  journal = {Experientia},
  year = {1990},
  volume = {46},
  pages = {372--378},
  number = {4}
}

@ARTICLE{SHAR90,
  author = {Kim A. Sharp and Barry Honig},
  title = {Electrostatic Interactions in Macromolecules: Theory and Applications},
  journal = ARBBC,
  year = {1990},
  volume = {19},
  pages = {301--332}
}

@ARTICLE{ShHo90,
  author = {Sharp, K.A. and Honig, B.},
  title = {Calculating Total Electrostatic Energies with Nonlinear {P}oisson--{B}oltzmann
	Equation},
  journal = {J. Phys.\ Chem.},
  year = {1990},
  volume = {19},
  pages = {7684}
}

@ARTICLE{ShFB90,
  author = {P. W. Sharp and J. M. Fine and K. Burrage},
  title = {Two-stage and Three-stage Diagonally Implicit {\rm Runge-Kutta Nystr\"o
	m} Methods fo Orders Three and Four},
  journal = {IMA J. Numer. Anal.},
  year = {1990},
  volume = {10},
  pages = {489--504}
}

@ARTICLE{SiAM90,
  author = {J. J. Sines and S. A. Allison and J. A. McCammon},
  title = {Point Charge Distributions and Electrostatic Steering in Enzyme/Substrate
	Encounter: {B}rownian Dynamics of Modified Copper/Zinc Superoxide
	Dismutases},
  journal = {Biochemistry},
  year = {1990},
  volume = {29},
  pages = {9403--9412},
  number = {40}
}

@ARTICLE{SMAB90,
  author = {J.M. Smaby and H.L. Brockman},
  title = {Surface dipole moments of lipids at the argon-water interface. Similarities
	among glycerol-ester based lipids},
  journal = BJ,
  year = {1990},
  volume = {58},
  pages = {195--204}
}

@ARTICLE{SMIT90A,
  author = {Jeremy Smith and Stephen Cusack and Bruce Tidor and Martin Karplus},
  title = {Inelastic Neutron Scattering Analysis of Low-Frequency Motions in
	Proteins: Harmonic and Damped Harmonic Models of Bovine Pancreatic
	Trypsin Inhibitor},
  journal = JCP,
  year = {1990},
  volume = {93},
  pages = {2974--2991}
}

@ARTICLE{SMITH90,
  author = {J.~Smith and K.~Kuczera and M.~Karplus},
  title = {Dynamics of Myoglobin: Comparison of Simulation Results with Neutron
	Scattering Spectra},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {1601--1605}
}

@ARTICLE{SOMP90,
  author = {H. Sompolinsky and D. Golomb and D. Kleinfeld},
  title = {Global processing of visual stimuli in a neural network of coupled
	oscillators},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {7200--7204}
}

@INBOOK{SpGr90,
  chapter = {28},
  pages = {287--296},
  title = {Recent Developments in Molecular Diversity: Computational Approaches
	to Combinatorial Chemistry},
  publisher = {Academic Press},
  year = {1990},
  author = {D.~C. Spellmeyer and P.~D.~J. Grootenhuis},
  series = {Annual Reports in Medicinal Chemistry}
}

@ARTICLE{SRIN90,
  author = {J.~Srinivasan and J.~M.~Withka and D.~L.~Beveridge},
  title = {Molecular dynamics of an {\it in vacuo} model of duplex d({CGCGAATTCGCG})
	in the B-form based on the amber3.0 force field},
  journal = BJ,
  year = {90},
  volume = {58},
  pages = {533--547},
  annote = {100\ps 300K, shift to A-form DNA, widening major and narrow minor
	groove, solvated with NA 6\AA along O-P-O that has +1 charge, 5\AA
	L-J and well depth of .1kcal/mol, and 131AMU, distance dependent
	dielectric, no-cutoff}
}

@ARTICLE{STAL90,
  author = {J. P. Staley and P. S. Kim},
  title = {Role of a Subdomain in the Folding of Bovine Pancreatic Trypsin Inhibitor},
  journal = NAT,
  year = {1990},
  volume = {344},
  pages = {62--67},
  annote = {BPTI}
}

@ARTICLE{STEI90,
  author = {T. A. Steitz},
  title = {Structural studies of protein-nucleic acid interaction: {The} source
	of sequence-specific binding},
  journal = QRB,
  year = {1990},
  volume = {23},
  pages = {205--280}
}

@ARTICLE{STRA90,
  author = {T. P. Straatsma and J. A. McCammon},
  title = {{ARGOS}, a Vectorized General Molecular Dynamics Program},
  journal = JCC,
  year = {1990},
  volume = {11},
  pages = {943--951},
  number = {8}
}

@ARTICLE{SUBR87,
  author = {S.~Subramaniam and T.~Marti and H.G.~Khorana},
  title = {blue membrane formation at low {pH} through protonation of ASP-85},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {1013--1017}
}

@ARTICLE{SUBR90A,
  author = {S. Subramaniam and T. Marti and H. G. Khorana},
  title = {Protonation State of {Asp} {(Glu)}-85 Regulates the Purple-to-Blue
	Transition in Bacteriorhodopsin Mutants {Arg}-82 $\rightarrow$ {Ala}
	and {Asp}-85 $\rightarrow$ {Glu}: The Blue Form is Inactive in Proton
	Translocation},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {1013--1017}
}

@ARTICLE{SUBR90,
  author = {P.~S.~Subramanian and S.~Pitchumani and D.~L.~Beveridge and H.~M.Berman},
  title = {A {M}onte {C}arlo Simulation Study of the Aqueous Hydration of r({G}p{C})$_2$:
	Comparison with Crystallographic Ordered Water Sites},
  journal = BP,
  year = {1990},
  volume = {29},
  pages = {771--783},
  annote = {amber3.0, 542 waters for the dinucleotide,periodic bndies, identifies
	water bridges}
}

@INPROCEEDINGS{SWOF90,
  author = {D. L. Swofford and G. J. Olsen},
  title = {Phylogeny reconstruction},
  booktitle = {Molecular Systematics},
  year = {1990},
  editor = {D. Hillis and C. Moritz},
  pages = {411--501},
  address = {Sunderland, MA},
  publisher = {Sinauer Associates}
}

@MANUAL{TERS90,
  title = {{DTM - Data Transfer Mechanism}},
  author = {J. Terstriep},
  organization = {Network Development Group, NCSA},
  year = {1990},
  note = {Available via anonymous ftp from ftp.ncsa.uiuc.edu}
}

@ARTICLE{TESC90,
  author = {Markus Tesch and Klaus Schulten},
  title = {A Simulated Cooling Process for Proteins},
  journal = CPL,
  year = {1990},
  volume = {169},
  pages = {97--102},
  number = {{1,2}},
  annote = {May 25, 1990}
}

@ARTICLE{TIRA90,
  author = {J. Tirado-Rives and W. L. Jorgensen},
  title = {Molecular Dynamics of Proteins with the {OPLS} Potential Functions.
	Simulation of the Third Domain of Silver Pheasant Ovomucoid in Water},
  journal = JACS,
  year = {1990},
  volume = {112},
  pages = {2773--2781}
}

@ARTICLE{TITT90,
  author = {J.~Tittor and D.~Oesterhelt},
  title = {The quantum yield of bacteriorhodopsin},
  journal = FEBS,
  year = {1990},
  volume = {263},
  pages = {269--273}
}

@ARTICLE{TRAU90,
  author = {J.K. Trautmann and A.P. Shreve and C.A. Violette and H. A. Frank
	and T.G. Owens and A.C. Albrecht},
  title = {Femtosecond dynamics of energy transfer in B800--850 light-harvesting
	complexes of {\em {R}hodobacter sphaeroides}},
  journal = {Proc.~Natl.~Acad.~Sci.~USA},
  year = {1990},
  volume = {87},
  pages = {215--219}
}

@ARTICLE{TRIS90,
  author = {Trissl, H.W.},
  title = {Photoelectric measurements of purple membranes},
  journal = PCPB,
  year = {1990},
  volume = {51},
  pages = {793--818}
}

@ARTICLE{TRUS90,
  author = {V. M. Trusova and V. V. Mezentsev and S. M. Ksenzenko and A. N. Tikhonov
	and M. I. Molchanov},
  title = {Phospholipids of the Thylakoid Membranes of Chloroplasts Devoid of
	Photosystem {II}},
  journal = BCH,
  year = {1990},
  volume = {55},
  pages = {355--362},
  number = {3},
  annote = {not relevant},
  keywords = {thylakoids; photosystem II; phospholipids; experimental},
  part = {2}
}

@ARTICLE{TULL90,
  author = {J. C. Tully},
  title = {Molecular Dynamics With Electronic Transitions},
  journal = JCP,
  year = {1990},
  volume = {93},
  pages = {1061--1071}
}

@ARTICLE{VARO90A,
  author = {G. V\'{a}r\'{o} and A. Duschl and J. K. Lanyi},
  title = {Interconversions of the {M}, {N}, and {O} Intermediates in the Bacteriorhodopsin
	Photocycle},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {3798--3804}
}

@ARTICLE{VARO90,
  author = {G. V\'{a}r\'{o} and J. K. Lanyi},
  title = {Protonation and Deprotonation of the {M}-Intermediate, {N}-Intermediate,
	and {O}-Intermediate During the Bacteriorhodopsin Photocycle},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {6858--6865}
}

@ARTICLE{VARO90B,
  author = {G. V\'{a}r\'{o} and J. K. Lanyi},
  title = {Pathways of the Rise and Decay of the {M} Photointermediate(s) of
	Bacteriorhodopsin},
  journal = BCH,
  year = {1990},
  volume = {29},
  pages = {2241--2250}
}

@BOOK{Verh90,
  title = { Nonlinear differential equations and dynamical systems},
  publisher = {Springer-Verlag},
  year = {1990},
  author = { Ferdinand Verhulst},
  address = { Berlin},
  nremark = { 277 p., SUBJECT: Differential equations, Nonlinear Differentiable
	dynamical systems, ISBN: 0387506284, Translation of: Nietlineaire
	differentiaalvergelijkingen en dynamische systemen. 515.355V588N,
	understandable, discusses averaging and Hamiltonians}
}

@ARTICLE{VIST90,
  author = {M.R. Vist and J.H. Davis},
  title = {Phase equilibria of cholestral/dipalmitoylphosphatidylcholine mixtures:
	$^2$H nuclear magnetic resonance and differential scanning calorimetry},
  journal = BCH,
  year = {1990},
  volume = {24},
  pages = {251--464},
  annote = {Stiudies of choletral membrane Classic experimental. Maybe good for
	Sheng?}
}

@INCOLLECTION{WORG90,
  author = {F. W\"org\"otter and E. Niebur and C. Koch},
  title = {Modeling Visual Cortex, Hidden Anisotropy in an Isotropic Inhibitory
	Connection Scheme},
  booktitle = {Neuronal Networks for Sensory and Motor Systems},
  publisher = {Elsevier},
  year = {1990},
  editor = {R. Eckmiller}
}

@ARTICLE{HEFE90b,
  author = {J. Hefele Wald and E. Goormaghtigh and J. De Meutter and J.-M. Ruysschaert
	and A. Jonas},
  title = {Investigation of the Lipid Domains and Apolipoprotein Orientation
	in Reconstituted High Density Lipoproteins by Fluorescence and {IR}
	Methods},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {20044--20050}
}

@ARTICLE{HEFE90a,
  author = {J. Hefele Wald and E. S. Krul and A. Jonas},
  title = {Structure of Apolipoprotein {A-I} in Three Homogeneous Reconstituted
	High Density Lipoprotein Particles},
  journal = JBC,
  year = {1990},
  volume = {265},
  pages = {20037--20043}
}

@ARTICLE{WALK90,
  author = {R.A. Walker and E.D. Salmon and S.A. Endow},
  title = {The {{\em Drosophila claret}} segregation protein is a minus-end
	directed motor molecule},
  journal = NAT,
  year = {1990},
  volume = {347},
  pages = {780--782}
}

@UNPUBLISHED{WALS90,
  author = {L. L. Walsh and M. Bobak and A. R. Crofts},
  title = {Partition of Amino Acids into Secondary Structure is Biased by the
	Hydrophobic Effect},
  note = {(abstract and poster presented at the 4th. Symp. Protein Soc.)},
  year = {1990}
}

@INCOLLECTION{WALT90,
  author = {J\"org A. Walter and Helge Ritter and Klaus Schulten},
  title = {Non-Linear Prediction with Self-Organizing Maps},
  booktitle = {International Joint Conference on Neural Networks, San Diego, California},
  publisher = {The Institute of Electrical and Electronics Engineers},
  year = {1990},
  volume = {1},
  pages = {589--594},
  address = {New York}
}

@TECHREPORT{Wang90a,
  author = {D.-L. Wang},
  title = {On Symplectic Difference Schemes for \mbox{Hamiltonian} Systems},
  institution = {Konrad-Zuse-Zentrum \mbox{f\"ur} Informationstechnik},
  year = {1990},
  number = {Sc 90-6},
  address = {Berlin}
}

@TECHREPORT{Wang90b,
  author = {D.-L. Wang},
  title = {Symplectic Difference Schemes for Perturbed \mbox{Hamiltonian} Systems},
  institution = {Konrad-Zuse-Zentrum \mbox{f\"ur} Informationstechnik},
  year = {1990},
  number = {Sc 90-17},
  address = {Berlin}
}

@ARTICLE{JING90,
  author = {J. Wang and A. Pullman},
  title = {The intrinsic molecular potential of glyceryl monooleate layers and
	its effect on the conformation and orientation of an inserted molecule:
	example of gramicidin A},
  journal = BBA,
  year = {1990},
  volume = {1024},
  pages = {10--18}
}

@INPROCEEDINGS{Wars90,
  author = {A. Warshel},
  title = {Electrostatic Free Energy as the Fundamental Structure Function Correlator
	in Proteins: Some Perspectives from Microscopic Simulations of Proteins
	Functions},
  booktitle = {Modelling of Molecular Structures and Properties},
  year = {1990},
  editor = {J.-L. Rivail},
  pages = {515--526},
  address = {Amsterdam},
  publisher = {Elsevier Science Publishers},
  annote = {introductory; many refs; free energy plays key role in relating structure
	and function; explicite water with outer constraint layer 10--15\AA;
	cut-off is BAD: especially for large systems long range water-water
	interactions are important; activation barrier in Gramicidin could
	not be represented well; long range Coulomb {\em and} also the surrounding
	(membrane, water) are very important for free energy calculations
	to work},
  keywords = {free energy; solvent models; protein dipoles-Langevin dipoles; free
	energy perturbation; surface constraints; Ewald method; enzyme catalysis;
	ion channels; Gramicidin A; charge separation in photosynthetic systems;
	Rps. viridis},
  nremark = {Proceedings of an International Meeting},
  nseries = {Studies in Physical and Theoretical Chemistry},
  nvolume = {71}
}

@BOOK{WHIT90,
  title = {Cortical Circuits},
  publisher = {Birkh\"auser Publishing Company},
  year = {1990},
  author = {E. L. White},
  address = {New York}
}

@ARTICLE{WHIT90b,
  author = { S. P. White and D. L. Scott and Z. Otwinowski and M. H. Gelb and
	P. B. Sigler},
  title = {Crystal Structure of Cobra-Venom Phospholipase {A}$_2$ in a complex
	with a transition-State Analogue},
  journal = SCI,
  year = {1990},
  volume = {250},
  pages = {1560--1563}
}

@ARTICLE{WILK90,
  author = {W.W. Wilkerson},
  title = {Anti-inflammatory {PLA$_2$} inhibitors},
  journal = {Drug future},
  year = {1990},
  volume = {15},
  pages = {139--148},
  annote = {Drug Design}
}

@ARTICLE{WILT90,
  author = {W. Wiltschko and R. Wiltschko},
  title = {Magnetic orientation and celestial cues in migratory orientation},
  journal = {Experientia},
  year = {1990},
  volume = {46},
  pages = {342--351},
  number = {4}
}

@UNPUBLISHED{WiSc90,
  author = {A. Windemuth and K. Schulten},
  title = {Molecular Dynamics on the Connection Machine},
  note = {manuscript},
  year = {1990}
}

@INCOLLECTION{WOLY90A,
  author = {Peter G. Wolynes},
  title = {Spin Glass Ideas and the Protein Folding Problem},
  booktitle = {Spin Glasses and Biology},
  publisher = {World Scientific Press},
  year = {1990},
  editor = {Daniel Stein}
}

@MISC{WOLY90B,
  author = {P. G. Wolynes},
  title = {Search and Recognition: Spin Glass Engineering as an Approach to
	Protein Structure Prediction},
  year = {1990},
  note = {Carges Lectures}
}

@ARTICLE{YANG90,
  author = {J.T. Yang and W.M. Saxton and R.J. Stewart and E.C. Raff and L.S.B.
	Goldstein},
  title = {Evidence that the head of kinesin is sufficient for force generation
	and motility {\em in vitro}},
  journal = SCI,
  year = {1990},
  volume = {249},
  pages = {42--47}
}

@ARTICLE{Yosh90,
  author = {H. Yoshida},
  title = {Construction of Higher Order Symplectic Integrators},
  journal = {Phys. Lett. A},
  year = {1990},
  volume = {150},
  pages = {262--268}
}

@ARTICLE{Zhou90,
  author = {H.-X. Zhou},
  title = {On the Calculation of Diffusive Reaction Rates Using {B}rownian Dynamics
	Simulations},
  journal = {J. Phys.\ Chem.},
  year = {1990},
  volume = {92},
  pages = {3092--3095},
  number = {5}
}

@ARTICLE{AUSI92,
  author = {J.~Ausio},
  title = {Structure and dynamics of transcriptionally active chromatin},
  journal = {J.\ Cell Sci.},
  year = {199},
  volume = {102},
  pages = {1--5},
  annote = {torsional stress responsible due to topos activity is responsible
	of nuclease hypersensitivity of transcriptionally active chromatin
	great review with pointers to top actvity}
}

@ARTICLE{THUN90,
  author = {M. M. G. M. Thunnissen and E. Ab and K. H. Kolk and A. Drenth and
	B. W. Dijkstra and O. P. Kuipers and R. Dijkman and G. H. de Haas
	and H. M. Verheij},
  title = {X-ray structure of phospholipase {A}$_2$ complexed with a substrate-derived
	inhibitor},
  journal = NAT,
  year = {19890},
  volume = {347},
  pages = {689--691}
}

@INPROCEEDINGS{MING89,
  author = {Ming, O. and Pique, M. and Hughes, J. and Brooks, F.},
  title = {Force Display Performs Better than Visual Display in a Simple 6-D
	Docking Task},
  booktitle = {Proc. of the IEEE Robotics and Automation Conference 4},
  year = {1989},
  month = MAY
}

@ARTICLE{DEGR89,
  author = {H. J. M. {de Groot} and G. S. Harbison and J. Herzfeld and R. G.
	Griffin},
  title = {Nuclear Magnetic-Resonance Study of the {Schiff}-Base in Bacteriorhodopsin\
	--\ Counterion Effects on the $^{15}${N} Shift Anisotropy},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {3346--3353}
}

@ARTICLE{VLIE89,
  author = {J. {de Vlieg} and H. J. C. Berendsen and W. F. van Gunsteren},
  title = {An {NMR}-based molecular dynamics simulation of the interaction of
	the {\em lac} repressor headpiece and its operator in aqueous solution},
  journal = PRO,
  year = {1989},
  volume = {6},
  pages = {104--127}
}

@ARTICLE{AbMa89,
  author = {R. A. Abagyan and V. N. Maiorov},
  title = {An Automatic Search for Similar Spatial Arrangements of $\alpha$-Helices
	and $\beta$-Strands in Globular Proteins},
  journal = JBSD,
  year = {1989},
  volume = {6},
  pages = {1045--1060}
}

@ARTICLE{Agarwal,
  author = {A. Agarwal},
  title = {{Performance Tradeoffs in Multithreaded Processors}},
  journal = {Private Communication},
  year = {1989}
}

@ARTICLE{AHN89,
  author = {C. B. Ahn and Z. H. Cho},
  title = {A generalized formulation of diffusion effects in $\mu$m resolution
	nuclear magnetic resonance imaging},
  journal = {Med. Phys.},
  year = {1989},
  volume = {16},
  pages = {22--28},
  brief = {analytical calculations},
  keywords = {paramagnetic contrast agent}
}

@ARTICLE{ALBE89,
  author = {A. Albeck and N. Friedman and M. Sheves and M. Ottolenghi},
  title = {Factors Affecting the Absorbtion Maxima of Acidic forms of Bacteriorhodopsin},
  journal = BJ,
  year = {1989},
  volume = {56},
  pages = {1259--1265}
}

@ARTICLE{AlYL89,
  author = {Allinger, Norman L. and Yuh, Young H. and Lii, Jen-Huei},
  title = {Molecular Mechanics. The MM3 force field for Hydrocarbons. (1)},
  journal = {Journal of the American Chemical Society},
  year = {1989},
  volume = {111},
  pages = {8551--8565},
  number = {23},
  nremark = {molecular mechanics, introduction, force field, MM3, aliphatic hydrocarbons,
	structural energy, heat of formation}
}

@ARTICLE{ALMS89,
  author = {Markus van Almsick and Klaus Schulten},
  title = {Mathematica: Mathematik auf {M}ikrocomputern},
  journal = MCM,
  year = {1989},
  volume = {11},
  pages = {42--59}
}

@ARTICLE{VALM89,
  author = {Markus van Almsick and Klaus Schulten},
  title = {Mathematica: Mathematik auf {M}ikrocomputern},
  journal = MCM,
  year = {1989},
  volume = {11},
  pages = {42--59}
}

@ARTICLE{ANDE89,
  author = {B. F. Anderson and H. M. Baker and G. E. Norris and D. W. Rice and
	E. N. Baker},
  title = {Structure of Human Lactoferrin},
  journal = JMB,
  year = {1989},
  volume = {209},
  pages = {711--734}
}

@BOOK{Arno89,
  title = {Mathematical Methods of Classical Mechanics},
  publisher = {Springer-Verlag},
  year = {1989},
  author = {V.~I. Arnold},
  address = {New York},
  edition = {2nd}
}

@ARTICLE{Asch89,
  author = {U. Ascher},
  title = {On symmetric schemes and differential-algebraic equations},
  journal = SJSSC,
  year = {1989},
  volume = {10},
  pages = {937--949}
}

@ARTICLE{ATKI89,
  author = {G. H. Atkinson and T. L Brack and D. Blanchard and G. Rumbles},
  title = {Picosecond Time-Resolved Resonance Raman Spectroscopy of the Initial
	Trans to Cis Isomerization in the Bacteriorhodopsin Photocycle},
  journal = CP,
  year = {1989},
  volume = {131},
  pages = {1--15}
}

@ARTICLE{BAAS85,
  author = {T. Baasov and M. Sheves},
  title = {Model Compounds for the Study of Spectroscopic Propeties of Visual
	Pigments and Bacteriorhodopsin},
  journal = JACS,
  year = {1989},
  volume = {107},
  pages = {7524--7533}
}

@ARTICLE{BAAS87A,
  author = {T. Baasov and M. Sheves},
  title = {Probing the Binding Site of Bacteriorhodopsin with a Fluorescent
	Chromophore},
  journal = JACS,
  year = {1989},
  volume = {109},
  pages = {1594--1596}
}

@ARTICLE{BACI89,
  author = {G. Bacic and M. R. Niesman and R. L. Magin and H. M. Swartz},
  title = {{NMR and ESR Study of Liposome Delivery of ${\rm Mn^{2+}}$ to Murine
	Liver}},
  journal = MRM,
  year = {1989},
  volume = {{\bf 13}},
  pages = {44--61},
  keywords = {paramagnetic contrast agent}
}

@ARTICLE{BADE89,
  author = {J. S. Bader and David Chandler},
  title = {Computer Simulation of Photochemically Induced Electron Transfer},
  journal = CPL,
  year = {1989},
  volume = {157},
  pages = {501--504}
}

@INPROCEEDINGS{BART79,
  author = {J.E. Bartmess and R.T. {McIver Jr.}},
  title = {The gas-phase acidity scale},
  booktitle = {Gas Phase Ion Chemistry},
  year = {1989},
  editor = {M.T. Browers},
  volume = {2},
  pages = {87--112},
  publisher = {Academic Press},
  annote = {get it!}
}

@ARTICLE{BEAT89,
  author = {M.~Beato},
  title = {Gene regulation by steroid hormones.},
  journal = {CELL},
  year = {1989},
  volume = {56},
  pages = {335--344},
  annote = {this is a review of HRE's, see also the book by martinez, MART91A}
}

@ARTICLE{BERG89,
  author = {H. Bergstr{\"o}m and R. {van Grondelle} and V. Sundstr{\"o}m},
  title = {Characterization of excitation energy trapping in photosynthetic
	purple bacteria at 77 K},
  journal = FEBS,
  year = {1989},
  volume = {250},
  pages = {503--508}
}

@ARTICLE{BEVE89,
  author = {D. L. Beveridge and F. M. DiCapua},
  title = {FREE ENERGY VIA MOLECULAR SIMULATION: Applications to Chemical and
	Biological Systems},
  journal = ARBBC,
  year = {1989},
  volume = {18},
  pages = {431--492},
  annote = {very good review article, explains all the basics, tons of citations;
	the problem of free energy is the slow convergence; slow growth:
	vary \lambda\ continously in the simulation to save time; typical
	sampling time is 10ps...100ps; absolute free energy of liquid water:
	-5.74kcal/mol (exp.); surface tension of water @ 305K: 0.071 N/m;
	united atom model could be a problem if entropy is to be calculated},
  keywords = {convergence of means (energy, ...); coupling parameter approach; pertubation
	method; thermodynamic integration; potential of mean force; close
	encounters; umbrella sampling; probability ratio method; thermodynamic
	cycle integration; Born equation; Onsager equation; PDLD: protein
	dipoles/Langevin dipoles; photosynthetic reaction center}
}

@ARTICLE{BIAN89,
  author = {M. E. Bianchi and M. Beltrame and L. Falciola},
  title = {Specific recognition of cruciform {DNA} by nuclear protein {HMG1}},
  journal = SCI,
  year = {1989},
  volume = {243},
  pages = {1056--1059}
}

@ARTICLE{BIRG89,
  author = {R.~R.~Birge and T.~M.~Cooper and C.~M.~Einterz and A.~F.~Lawrence
	and M.~B.~Masthay and A.~Schick and C.~Vasilakis and C.~F.~Zhang
	and R.~Zidovetzki},
  title = {A spectroscopic, photocalorimetric and theoretical investigation
	of the quantum efficiency of the primary event in bacteriorhodopsin},
  journal = JACS,
  year = {1989},
  volume = {111},
  pages = {4063--4073}
}

@ARTICLE{BITT89,
  author = {Robert Bittl and Klaus Schulten},
  title = {A Static Ensemble Approximation for Stochastically Modulated Quantum
	Systems},
  journal = JCP,
  year = {1989},
  volume = {90},
  pages = {1794--1803}
}

@ARTICLE{BRAC89,
  author = {T. L. Brack and G. H. Atkinson},
  title = {Picosecond Time-resolved resonance raman spectrum of the K-590 Intermediate
	in the Room Temperature Bacteriorhodopsin Photocycle},
  journal = JMS,
  year = {1989},
  volume = {214},
  pages = {289--303}
}

@INPROCEEDINGS{Bran89,
  author = {A. Brandt},
  title = {The {W}eizmann {I}nstitute Research in Multilevel Computations: 1988
	Report},
  booktitle = {Proc. of the Fourth Copper Mountain Conference on Multigrid methods},
  year = {1989},
  editor = {J. Mandel and S. F. McCormick and J. E. Dendy,~Jr. and C. Farhat
	and G. Lonsdale and S. V. Parter and J. W. Ruge and K. St\mbox{\"u}ben},
  address = {Philadelphia},
  organization = {SIAM}
}

@BOOK{BrCP90,
  title = {Numerical Solution of Initial-Value Problems in Differential-Algebraic
	Equations},
  publisher = {North-Holland},
  year = {1989},
  author = {K.E. Brenan and S.L. Campbell and L.R. Petzold}
}

@ARTICLE{BREN89,
  author = {G.~A.~Brent and M.~K.~Dunn and J.~W.~Harney and T.~Gulick and P.~R.~Larsen},
  title = {Thyroid hormone aporeceptor represses {T}${_3}$ inducible promoters
	and blocks activity of the retinoic acid receptor.},
  journal = NB,
  year = {1989},
  volume = {1},
  pages = {329--336}
}

@ARTICLE{BRIN89,
  author = {Andrew T. Brint and Hazel M. Davies and Eleanor M. Mitchell and Peter
	Willett},
  title = {Rapid geometric searching in protein structures},
  journal = JMG,
  year = {1989},
  volume = {7},
  pages = {48--53}
}

@ARTICLE{BROO89,
  author = {C. L. Brooks and M. Karplus},
  title = {Solvent Effects on Protein Motion and Protein Effects on Solvent
	Motion: Dynamics of the Active Site Region of Lysozyme},
  journal = JMB,
  year = {1989},
  volume = {208},
  pages = {159--181}
}

@ARTICLE{BROO89A,
  author = {C.~L.~Brooks and M.~Karplus and B.~M.~Pettit},
  title = {Proteins: A theoretical perspective of dynamics, structure and thermodynamics},
  journal = {FIXME},
  year = {1989},
  address = {New York},
  editor = {J.~Wiley and Sons},
  publisher = {J.~Wiley \& Sons}
}

@ARTICLE{BRYN89,
  author = {J. D. Bryngelson and P. G. Wolynes},
  title = {Intermediates and Barrier Crossing in a Random Energy Model (with
	Applications to Protein Folding)},
  journal = {J. Phys. Chem.},
  year = {1989},
  volume = {93},
  pages = {6902}
}

@ARTICLE{BRUN89,
  author = {Axel Br{\"u}nger},
  title = {A Memory-Efficient Fast {Fourier} Transformation Algorithm for Crystallographic
	Refinement on Supercomputers},
  journal = {\it Acta Cryst.},
  year = {1989},
  volume = {A45},
  pages = {42--50}
}

@ARTICLE{BRUN89a,
  author = {A.T. Br{\"u}nger and M. Karplus and G. A. Petsko},
  title = {Crystallographic Refinement by Simulated Annealing: Application to
	a 1.5 \AA Resolution Structure of Crambin},
  journal = {\it Acta Cryst.},
  year = {1989},
  volume = {A45},
  pages = {50--61}
}

@BOOK{BUDA89,
  title = {{The {M}erck index: an encyclopedia of chemicals, drugs, and biologicals}},
  publisher = {Merck},
  year = {1989},
  author = {Susan Budavari and Maryadele J. O'Neil and Ann Smith},
  address = {Rahway, NJ}
}

@ARTICLE{BUHM89,
  author = {Joachim Buhmann and Robert Divko and Klaus Schulten},
  title = {Associative Memory with High Information Content},
  journal = PRA,
  year = {1989},
  volume = {39},
  pages = {2689--2692}
}

@INCOLLECTION{BUHM89A,
  author = {Joachim Buhmann and Robert Divko and Klaus Schulten},
  title = {On Sparsely Coded Associative Memories},
  booktitle = {Neural Networks: From Models to Applications, {N'EURO~'88}},
  publisher = {{EZIDET}},
  year = {1989},
  editor = {L. Personnaz and G. Dreyfus},
  pages = {360--371},
  address = {Paris}
}

@ARTICLE{CARL89,
  author = {M.-F. Carlier},
  title = {Role of Nucleotide Hydrolysis in the Dynamics of Actin Filaments
	and Microtubules},
  journal = IRC,
  year = {1989},
  volume = {115},
  pages = {139--170}
}

@ARTICLE{CARR89,
  author = {Nicholas Carriero and David Gelernter},
  title = {How to Write Parallel Programs: A Guide to the Perplexed},
  journal = ACMCS,
  year = {1989},
  volume = {21},
  pages = {323--357},
  number = {3},
  keywords = {Linda; parallel programming methodology; parallelism; result parallelism;
	agenda parallelism; specialist parallelism}
}

@ARTICLE{CARR89A,
  author = {N. Carriero and D. Gelernter},
  title = {Linda in Context},
  journal = {Comm.\ ACM},
  year = {1989},
  volume = {(32,4)},
  pages = {444--458}
}

@ARTICLE{CART89,
  author = {B. Cartling},
  title = {From Short-Time Molecular Dynamics to Long-Time Stochastic Dynamics
	of Proteins},
  journal = JCP,
  year = {1989},
  volume = {91},
  pages = {427--438}
}

@ARTICLE{CHAN89,
  author = {David Chandler},
  title = {Computer Simulation of Electron Transfer},
  journal = CS,
  year = {1989},
  volume = {29A},
  pages = {61--62}
}

@ARTICLE{Chen89,
  author = {R. Chen},
  title = {{M}onte {C}arlo Simulations for the Study of Hemoglobin-Fragment
	Conformations},
  journal = {J. Comp. Chem.},
  year = {1989},
  volume = {10},
  pages = {488--494}
}

@ARTICLE{CHIU89,
  author = {S. W. Chiu and S. Subramaniam and E. Jakobsson and J. A. McCammon},
  title = {Water and polypeptide conformations in the gramicidin channel. A
	molecular dynamics study},
  journal = {Biophys. J.},
  year = {1989},
  volume = {56},
  pages = {253--261},
  annote = {requested Tx=19920924.}
}

@ARTICLE{Cole89,
  author = {John P. Coleman},
  title = {Numerical Methods for $y'' = f(x, y)$ Via Rational Approximations
	for the Cosine},
  journal = {IMA J. Numer.\ Anal.},
  year = {1989},
  volume = {9},
  pages = {145--165}
}

@ARTICLE{CrGo89,
  author = {Michael Creutz and Andreas Gocksch},
  title = {Higher-Order Hybrid {M}onte {C}arlo Algorithms},
  journal = PRL,
  year = {1989},
  volume = {63},
  pages = {9--12},
  number = {1}
}

@ARTICLE{CrFV89,
  author = {Andrea Crisanti and Massimo Falcioni and Angelo Vulpiani},
  title = {On the effects of an uncertainty on the evolution law in dynamical
	systems},
  journal = phya,
  year = {1989},
  volume = {160},
  pages = {482--502},
  nremark = {... The evolution law of chaotic dynamical systems ... In spite of
	the short predictablity time $t_p$ on a single trajectory we found
	that the statistical properties are not sensitive to small changes
	in the evolution law ... This feature holds also for correlation
	funcitons at a delay larger than $t_p$. The authors uses the Lorenz
	equations as an example.}
}

@ARTICLE{DAMM89,
  author = {K.~Damm and C.~C.~Thompson and R.~M.~Evans},
  title = {Protein encoded by \mbox{v--{\em erb}{A}} functions as a thyroid--hormone
	receptor antagonist.},
  journal = NAT,
  year = {1989},
  volume = {339},
  pages = {593--597}
}

@ARTICLE{DANI89,
  author = {M.~Danielsen and L.~Hinck and G.~M.~Ringold},
  title = {Two amino acids within the knuckle of the first zinc finger specify
	{DNA} response element activation by the glucocorticoid receptor},
  journal = {Cell},
  year = {1989},
  volume = {57},
  pages = {1131--1138},
  annote = {see above}
}

@ARTICLE{DAOP89,
  author = {S.\ Dao-Pin and D.\ I.\ Liao and S.\ J.\ Remington},
  title = {Electrostatic Fields in the Active Sites of Lysozymes},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {5361--5365}
}

@ARTICLE{DEIS89,
  author = {J. Deisenhofer and H. Michel},
  title = {The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas
	viridis},
  journal = {Angewandte Chemie},
  year = {1989},
  volume = {28},
  pages = {829--?}
}

@ARTICLE{DENC89,
  author = {N. A. Dencher and D. Dresselhaus and G. Zacca{\"{\i}} and G. B{\"u}ldt},
  title = {Structural Changes in Bacteriorhodopsin During Proton Translocation
	Revealed by Neutron Diffraction},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {7876--7879}
}

@ARTICLE{DRAK89,
  author = {B. Drake and C. B. Prater and A. L. Weisenhorn and S. A. C. Gould
	and T. R. Albrecht and C. F. Quate and D. S. Channell and H. G. Hansma
	and P.K Hansma},
  title = {Imaging Crystals, Polymers, and Processes in Water with the Atomic
	Force Microscope},
  journal = SCI,
  year = {1989},
  volume = {243},
  pages = {1586},
  annote = {june 1}
}

@ARTICLE{DZWI89,
  author = {Witold Dzwinel and Monika Bargiel and Jacek Kitowski and Jacek Mo\'{s}ci\'{n}ski},
  title = {Linked Lists and the Method of Lights in Molecular Dynamics Simulation
	--- Search for the Best Method of Forces Evaluation in Sequential
	Code},
  journal = MS,
  year = {1989},
  volume = {4},
  pages = {229--239},
  annote = {short range IA only (cut-offs); deals mainly with memory-efficient
	build-up of neighbor lists; gives long program listings; methods
	of lights finds neighbors using a cubical grid and sorting the coordinates
	along the x, y, and z direction},
  keywords = {linked lists; method of lights; forces evaluation; list processing;
	vector computers; IBM-PC/AT; LJ-liquid}
}

@ARTICLE{DER89,
  author = {A. D{\'e}r and R. T{\'o}th-Bocon{\'a}di and L. Keszthelyi},
  title = {Bacteriorhodopsin as a Possible Chloride Pump},
  journal = FEBS,
  year = {1989},
  volume = {259},
  pages = {24--26}
}

@ARTICLE{ECKH89,
  author = {R. Eckhorn and R. Bauer and W. Jordan and M. Brosch and W. Kruse
	and M. Munk and H. J. Reitboeck},
  title = {Coherent oscillations: {A} mechanism of feature linking in the visual
	cortex? Multiple electrode and correlation analysis in the cat},
  journal = {Biol. Cybernetics},
  year = {1989},
  volume = {60},
  pages = {121--130}
}

@ARTICLE{ELSA89,
  author = {M. A. El-Sayed and C. T. Lin and W. R. Mason},
  title = {Is There an Excitonic Interaction or Antenna System in Bacteriorhodopsin?},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {5376--5379}
}

@ARTICLE{FAHM89,
  author = {K. Fahmy and F. Siebert and M. Grossjean and P. Tavan},
  title = {Photoisomerization in Bacteriorhodopsin Studied by {FTIR}, Linear
	Dichroism and Photoselection Experiments Combined With Quantum Chemical
	Theoretical Analysis},
  journal = JMS,
  year = {1989},
  volume = {214},
  pages = {257--288}
}

@ARTICLE{FARC89,
  author = {J.W. Farchaus and D. Oesterhelt},
  title = {A {{\em {R}hodobacter sphaeroides puf}}{ L, M, and X} deletion mutant
	and its complementation in trans with a 5.3 kb {\em puf} operon shuttle
	fragment},
  journal = EMBO,
  year = {1989},
  volume = {8},
  pages = {47--54}
}

@ARTICLE{FASM89,
  author = {Gerald D. Fasman},
  title = {Protein conformation prediction},
  journal = TIBS,
  year = {1989},
  volume = {14},
  pages = {295--299}
}

@ARTICLE{FeWQ89,
  author = {K. Feng and H.-M. Wu and M.-Z. Qin and D.-L. Wang},
  title = {Construction of Canonical Difference Schemes for \mbox{Hamiltonian}
	Formalism via Generating Functions},
  journal = {J. Comput. Math.},
  year = {1989},
  volume = {11},
  pages = {71--95},
  number = {1}
}

@ARTICLE{FENG89,
  author = {Y. Feng and H. Roder and S. W. Englander and A. J. Wand and D. L.
	DiStefano},
  title = {Proton Resonance Assignments of Horse Ferricytochrome~C},
  journal = {Biochemistry},
  year = {1989},
  volume = {28},
  pages = {195--203}
}

@ARTICLE{FERS89,
  author = {Alan R.\ Fersht and Michael J.\ E.\ Sternberg},
  title = {Can a simple function for the dielectric response model electrostatic
	effects in globular proteins?},
  journal = {Prot.\ Eng.},
  year = {1989},
  volume = {2},
  pages = {527--530}
}

@ARTICLE{FILM89,
  author = {D.~J.~Filman and R.~Syed and M.~Chow and A.~J.~Macadam and P.~D.~Minor
	and J.~M.~Hogle},
  title = {Structural factors that control conformational transitions and stereotypes
	specificity in type 3 poliovirus},
  journal = EMBO,
  year = {1989},
  volume = {8},
  pages = {1567--1579}
}

@ARTICLE{FLIT89,
  author = {Sabine L. Filtsch and H. Gobind Khorana},
  title = {Structural Studies on Transmembrane Proteins .1. {M}odel Study Using
	Bacteriorhodopsin Mutants Containing Single Cysteine Residues},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {7800--7805}
}

@ARTICLE{FlPe89,
  author = {H.\ Flyvbjerg and H.\ G.\ Petersen},
  title = {Error estimates on averages of correlated data},
  journal = JCP,
  year = {1989},
  volume = {91},
  pages = {461--466}
}

@ARTICLE{FREN89,
  author = {D. L. French and R. Laskov and M. D. Scharff},
  title = {The Role of Somatic Hypermutation in the Generation of Antibody Diversity},
  journal = SCI,
  year = {1989},
  volume = {244},
  pages = {1152--1157}
}

@ARTICLE{FAPN89,
  author = {D.A. Frenz and S.K. Akiyama and D.F Paulsen and S.A. Newman},
  title = {Latex beads as probes of cell surface-extracellular matrix interactions
	during chondrogenesis: evidence for a role for amino-terminal heparin-binding
	domain of fibronectin},
  journal = {Dev. Biol.},
  year = {1989},
  volume = {136},
  pages = {87--96}
}

@ARTICLE{FrJN89,
  author = {D.A. Frenz and N.S. Jaikaria and S.A. Newman},
  title = {The mechanism of precartilage mesenchymal condensation: a major role
	for interaction of the cell surface with the amino-terminal heparin-binding
	domain of fibronectin},
  journal = {Dev. Biol.},
  year = {1989},
  volume = {136},
  pages = {97--103}
}

@ARTICLE{FRIE89C,
  author = {N. Friedman and M. Sheves and M. Ottolenghi},
  title = {Model Systems for Rhodopsins: The Photolysis of Protonated Retinal
	Schiff Bases, Cyanine Dye, and Artificial Cyanine-Bacteriorhodopsin},
  journal = JACS,
  year = {1989},
  volume = {111},
  pages = {3203--3211}
}

@ARTICLE{FRIE89,
  author = {M. S. Friedrichs and P. G. Wolynes},
  title = {Toward Protein Tertiary Structure Recognition by Means of Associative
	Memory {Hamiltonian}s},
  journal = SCI,
  year = {1989},
  volume = {246},
  pages = {371--373}
}

@ARTICLE{FRIE89B,
  author = {M. S. Friedrichs and P. G. Wolynes},
  title = {Towards Protein Tertiary Structure Recognition by Means of Associative
	Memory {Hamiltonian}s},
  journal = SCI,
  year = {1989},
  volume = {246},
  pages = {371}
}

@ARTICLE{GAT91,
  author = {Y. Gat and M. Grossjean and I. Pinevsky and H. Takei and Z. Rothman
	and H. Sigrist and A. Lewis and M. Sheves},
  title = {Synthetic Retinals as Probes for the Binding Site and Photoreactions
	in Rhodopsin},
  journal = JMEB,
  year = {1989},
  volume = {112},
  pages = {193--212}
}

@BOOK{GENN89,
  title = {Biomembranes: Molecular Structure and Function},
  publisher = {Springer-Verlag},
  year = {1989},
  author = {Robert B. Gennis},
  address = {New York},
  annote = {THE membrane reference; cell-gennis.tiff from page 3; cell-protein-gennis.tiff
	from page 8},
  keywords = {membranes}
}

@ARTICLE{GERW89,
  author = {K. Gerwert and B. Hess and J. Soppa and D. Oesterhelt},
  title = {Role of {Asp}-96 in Proton Translocation by Bacteriorhodopsin},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {4943--4947}
}

@ARTICLE{GILB89,
  author = {C. D. Gilbert and T. N. Wiesel},
  title = {Columnar Specificity of Intrinsinc Horizontal and Corticocortical
	Connections in Cat Visual Cortex},
  journal = {J. Neurosci.},
  year = {1989},
  volume = {9},
  pages = {2432--2442}
}

@ARTICLE{Glas89,
  author = {?? L.J. Glass},
  title = {temperature echos},
  journal = {solid State Commun.},
  year = {1989},
  volume = {36},
  pages = {875}
}

@ARTICLE{GRAY89,
  author = {Charles M. Gray and Wolf Singer},
  title = {Stimulus-specific neuronal oscillations in orientation columns of
	cat visual cortex},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {1698--1702}
}

@ARTICLE{GREE89,
  author = {L. Greengard and W. D. Gropp},
  title = {A parallel version of the fast multipole method},
  journal = {Parallel Processing for Scientific Computing},
  year = {1989},
  address = {SIAM: Philadelphia}
}

@ARTICLE{GROS89,
  author = {Michael F. Grossjean and Paul Tavan and Klaus Schulten},
  title = {Can Normal Mode Analysis Reveal the Geometry of the {L}$_{550}$ Chromophore
	of Bacteriorhodopsin?},
  journal = EBJ,
  year = {1989},
  volume = {16},
  pages = {341--349}
}

@MASTERSTHESIS{Grub89,
  author = {H. Grubm{\"u}ller},
  title = {\mbox{D}ynamiksimulation sehr gro\ss er \mbox{Makromolek\"ule} auf
	einem \mbox{Parallelrechner}},
  school = {\mbox{Physik-Dept. der Tech. Univ. M\"unchen}},
  year = {1989},
  address = {Munich}
}

@MASTERSTHESIS{GRUB89A,
  author = {Helmut Grubm{\"u}ller},
  title = {Dynamiksimulation sehr gro\ss er Makromolek\"ule auf einem Parallelrechner},
  school = {{T}echnische {U}niversit\"at {M}\"unchen, {P}hysik-Department, T~30},
  year = {1989},
  type = {Diplomarbeit},
  address = {James-Franck-Stra{\ss}e, 8046~Garching},
  annote = {This is the GERMAN version}
}

@ARTICLE{GRUE85,
  author = {D.W.R Gruen},
  title = {A model for the chains in amphiphilic aggregates. 1: Comparison with
	a molecular dynamics simulation of a bilayer},
  journal = JPC,
  year = {1989},
  volume = {89},
  pages = {146--153}
}

@ARTICLE{GUST89,
  author = {T.~A.~Gustafson and A.~Taylor and L.~Kedes},
  title = {{\sc DNA} bending is induced by a transcription factor that interacts
	with the human c-Fos and $\alpha$--actin promoters.},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {2162--2166},
  annote = {says that eukaryotic transcription activator bends DNA, not read}
}

@ARTICLE{HA89,
  author = {J-H.~Ha and R.~S.~Spolar and M.~T.~Record},
  title = {Role of the hydrophobic effect in stability of site-specific protein-{DNA}
	complexes.},
  journal = JMB,
  year = {1989},
  volume = {209},
  pages = {801--816}
}

@ARTICLE{HARA89,
  author = {S. Hara and I. Kudo and H. W. Chang and K. Matsuata and T. Miyamoto
	and K. Inoue},
  title = {Purification and characterization of Extracellular Phospholipase
	{A$_2$} from Human Synovial Fluid in rheumatoid arthritis},
  journal = JB,
  year = {1989},
  volume = {105},
  pages = {395--399},
  annote = {title says it. already got it.}
}

@ARTICLE{HARD89,
  author = {P. A. Hardy and R. M. Henkelman},
  title = {Transverse Relaxation Rate Enhancement Caused by Magnetic Particulates},
  journal = {Magnetic Resonance in Medicine},
  year = {1989},
  volume = {7},
  pages = {265--275},
  brief = {Some simulations (1/T2) were done to complement their experiments
	which measure 1/T1 and 1/T2 in agar for various concentrations of
	1 micron ferrite particles. Explicit values of 1/T1 enhancement as
	well as 1/T2 are given. Why don't we do our DIPOLE simulations to
	calculate 1/T1 effects? They give a value of the magnetic moment
	due to a ferrite particle.},
  keywords = {simulation}
}

@ARTICLE{Harv89,
  author = {Harvey, S. C.},
  title = {Treatment of Electrostatic Effects in Macromolecular Modeling},
  journal = {Proteins},
  year = {1989},
  volume = {5},
  pages = {78}
}

@ARTICLE{HO89,
  author = {Ming-Tao P. Ho and John B. Massey and Henry J. Pownall and Robert
	E. Anderson and Joe G. Hollyfield},
  title = {Mechanism of Vitamin {A} Movement between Rod Outer Segments, Interphotoreceptor
	Retinoid-binidng Protein, and Liposomes},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {928--935}
}

@ARTICLE{HOFR89,
  author = {J. Hofrichter and E. R. Henry and R. H. Lozier},
  title = {Photocycle of Bacteriorhodopsin in Light- and Dark-adapted Purple
	Membrane Studied by Time-resolved Absorption Spectroscopy},
  journal = BJ,
  year = {1989},
  volume = {56},
  pages = {693--706}
}

@ARTICLE{HOLL89,
  author = {Holley, L. H. and Karplus, M.},
  title = {Protein secondary structure prediction with a neural network},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1989},
  volume = {86},
  pages = {152--156}
}

@ARTICLE{HOLZ89,
  author = {M. Holz and L. A. Drachev and T. Mogi and H. Otto and A. D. Kaulen
	and M. P. Heyn and V. P. Skulachev and H. G. Khorana},
  title = {Replacement of Aspartic Acid-96 by Asparagine in Bacteriorhodopsin
	Slows Both the Decay of the {M} Intermediate and the Associated Proton
	Movement},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {2167--2171}
}

@BOOK{HORO78,
  title = {Fundamentals of Computer Algorithms},
  publisher = {Computer Science Press},
  year = {1989},
  author = {E. Horowitz and S. Sahni},
  address = {Rockville, Maryland}
}

@ARTICLE{Houw89,
  author = {P. J. van der Houwen},
  title = {Stabilized Runge-Kutta Methods for Second Order Differential Equations
	without First Derivatives},
  journal = SJNA,
  year = {1989},
  volume = {16},
  pages = {523--537}
}

@ARTICLE{HOWA89,
  author = {J. Howard and A.J. Hudspeth and R.D. Vale},
  title = {Movement of microtubules by single kinesin molecules},
  journal = NAT,
  year = {1989},
  volume = {342},
  pages = {154--158}
}

@ARTICLE{HUST89,
  author = {Shawn E. Huston and Peter J. Rossky},
  title = {Free Energies of Association for the Sodiu,--Dimethyl Phosphate Ion
	Pair in Aqueous Solution},
  journal = JPC,
  year = {1989},
  volume = {93},
  pages = {7888--7895},
  annote = {timestep=2fs},
  keywords = {potential of mean force (PMF); truncation effects; minimum image mathods
	(MI)}
}

@BOOK{INMO89b,
  title = {The Transputer Application Notebook},
  publisher = {SGS Thomson},
  year = {1989},
  author = {INMOS},
  pages = {291--298}
}

@ARTICLE{JACO89,
  author = {R. E. Jacobs and S. H. White},
  title = {The nature of the hydrophobic binding of small peptides at the bilayer
	interface: implications for the insertion of transbilayer helices},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {3421--3437},
  annote = {requested Tx=19920908.}
}

@ARTICLE{JAIN89,
  author = {M. K. Jain and O.Berg},
  title = {Kinetics of interfacial catalysis by phospholipase {A}$_2$ and regulation
	of interfacial activation and inhibition},
  journal = BBA,
  year = {1989},
  volume = {1002},
  pages = {127--156},
  annote = {get it!}
}

@ARTICLE{JAIN89A,
  author = {S.~Jain and M.~Sundaralingam.},
  title = {Effect of crystal packing environment on conformation of the {DNA}
	duplex},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {12780--12784}
}

@ARTICLE{JONA89,
  author = {A. Jonas and K. E. Kezdy and J. H. Wald},
  title = {Defined Apolipoprotein {A-I} Conformations in Reconstituted High
	Density Lipoprotein Discs},
  journal = {J. Biol. Chem.},
  year = {1989},
  volume = {264},
  pages = {4818--4824}
}

@INPROCEEDINGS{JAHN89,
  author = {F. J{\"a}hnig},
  title = {Structure prediction for membrane proteins},
  booktitle = {Prediction of Protein Structure and the Principles of Protein Conformation},
  year = {1989},
  editor = {G.D. Fasman},
  pages = {707},
  address = {New York},
  publisher = {Plenum}
}

@ARTICLE{KaGo89,
  author = {N. Karawasa and W.~A. Goddard},
  title = {Acceleration of Convergence for Lattice Sums},
  journal = JPC,
  year = {1989},
  volume = {93},
  pages = {7320}
}

@ARTICLE{Katz89,
  author = {J. Katzenelson},
  title = {Computational Structure of the N-Body Problem},
  journal = SJSSC,
  year = {1989},
  volume = {10},
  pages = {787--815}
}

@INPROCEEDINGS{Kenn89,
  author = {A. D. Kennedy},
  title = {The theory of hybrid stochastic algorithms},
  booktitle = {Probabilistic Methods in quantum field theory and quantum gravity},
  year = {1989},
  editor = {P. H. Damgaard and H. H{\"u}ffel and A. Rosenblum},
  volume = {224},
  series = {{NATO ASI} Series},
  pages = {209},
  address = {New York},
  publisher = {Plenum Press}
}

@ARTICLE{KESZ89,
  author = {L. Keszthelyi and P. Ormos},
  title = {Proton Electric Response Signals from Dielectrically Polarized Systems},
  journal = JMEB,
  year = {1989},
  volume = {109},
  pages = {193--200}
}

@ARTICLE{KING89,
  author = {G. King and A. Warshel},
  title = {A surface constrained all-atom solvent model for effective simulations
	of polar solutions},
  journal = JCP,
  year = {1989},
  volume = {91},
  pages = {3647--3661}
}

@ARTICLE{KORN89B,
  author = {N. V. Korneeva and S. P. Balashov and F. F. Litvin},
  title = {Electron-Vibrational Spectra of Bacteriorhodopsin and the Intermediates
	of its Photochemical Cycle},
  journal = BM,
  year = {1989},
  volume = {6},
  pages = {290--300}
}

@ARTICLE{KORN89,
  author = {A.A. Kornyshev and S. Leikin},
  title = {Fluctuation theory of hydration forces: the dramatic effects of inhomogeneous
	boundary conditions},
  journal = {Phys. Rev. A},
  year = {1989},
  volume = {40},
  pages = {6431--6437}
}

@ARTICLE{KRAM89,
  author = {R.M. Kramer and R.B. Pepinsky},
  title = {Structure and properties of a human non-pancreatic phospholipase
	{A}$_2$},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {5768--5775}
}

@ARTICLE{KUHN89,
  author = {G.~C.~Kuhnke and H.~J.~Theres and R.~Ehring},
  title = {{\sc RNA} polymerase and gal repressor bind simultaneously and with
	{\sc DNA} bending to the control region of {\it Escherichia coli}
	galactose operon},
  journal = EMBO,
  year = {1989},
  volume = {8},
  pages = {1247--1255},
  annote = {prokaryotic transcription activators that bend DNA, not read}
}

@ARTICLE{LAVE89,
  author = {R.~Lavery and H.~Sklenar},
  title = {Defining the structure of irregular nucleic acids: conventions and
	principles.},
  journal = {J.\ Biomol.\ Str.\ Dyn.},
  year = {1989},
  volume = {6},
  pages = {655--667},
  annote = {use as reference to MDtoolchest if analyzed DNA, add above also}
}

@BOOK{LAZA89,
  title = {Free Radicals in Chemistry and Biology},
  publisher = {CRC Press, Inc.},
  year = {1989},
  author = {M. Lazar and J. Rychly and V. Klimo and P. Pelikan and L. Valko},
  address = {Boca Raton, Fla.}
}

@ARTICLE{LEE89,
  author = {J.K. Lee and B.S. DeHoff and T.J. Donohue and R.I. Gumport and S.
	Kaplan},
  title = {Transcriptional analysis of puf operon expression in {{\em {R}hodobacter
	sphaeroides}} 2.4.1 and an intercistronic transcription terminator
	mutant},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {19354--65}
}

@ARTICLE{LEEM89,
  author = {Min S.~Lee and Garry P.~Gippert and Kizhake V.~Soman and David A.~Case
	and Peter E.~Wright},
  title = {Three-Dimensional Solution Structure of a Single Zinc Finger {\sc
	DNA}--Binding Doamin},
  journal = SCI,
  year = {1989},
  volume = {245},
  pages = {635--637},
  annote = {zinc finger TFIIIa}
}

@ARTICLE{LEVI89,
  author = {M. Levitt},
  title = {Molecular Dynamics of Macromolecules in Water},
  journal = {Chem.\ Scr.},
  year = {1989},
  volume = {29A},
  pages = {197--203}
}

@ARTICLE{LIN89A,
  author = {S. W. Lin and R. A. Mathies},
  title = {Orientation of the Protonated Retinal {Schiff} Base Group in Bacteriorhodopsin
	from Absorption Linear Dichroism},
  journal = BJ,
  year = {1989},
  volume = {56},
  pages = {653--660}
}

@ARTICLE{LoBr89,
  author = {Richard J. Loncharich and Bernhard R. Brooks},
  title = {The Effects of Truncating Long-Range Forces on Protein Dynamics},
  journal = {Proteins:\ Stru.\ Func.\ and Genetics},
  year = {1989},
  volume = {6},
  pages = {32--45},
  annote = {cut-off has dramatic effect on overall protein dynamics; compares
	rms fluctuations and rms deviation from no-cut-off simulation and
	from X-ray structure; VERY interesting paper; $\Delta t = 1fs$; Richard
	J. Loncharich works now for Ely Lilly and we cooperate with him},
  keywords = {long range truncation; molecular dynamics; carboxy-myoglobin; truncation
	effects; protein electrostatics; shifted potential; switching function;
	atom-atom truncation based on distance; atom-atom truncation based
	on a list; group-group truncation based on distance; group-group
	truncation based on a list; comparision of simulation results; error
	analysis}
}

@ARTICLE{LONC89,
  author = {Richard J. Loncharich and Bernhard R. Brooks},
  title = {The Effects of Truncating Long-Range Forces on Protein Dynamics},
  journal = PSFG,
  year = {1989},
  volume = {6},
  pages = {32--45},
  annote = {cut-off has dramatic effect on overall protein dynamics; compares
	rms fluctuations and rms deviation from no-cut-off simulation and
	from X-ray structure; VERY interesting paper; $\Delta t = 1fs$; Richard
	J. Loncharich works now for Ely Lilly and we cooperate with him},
  keywords = {long range truncation; molecular dynamics; carboxy-myoglobin; truncation
	effects; protein electrostatics; shifted potential; switching function;
	atom-atom truncation based on distance; atom-atom truncation based
	on a list; group-group truncation based on distance; group-group
	truncation based on a list; comparision of simulation results; error
	analysis}
}

@TECHREPORT{Mack89,
  author = {Paul B. Mackenzie},
  title = {An Improved Hybrid {M}onte {C}arlo Method},
  institution = {Fermi National Accelerator Laboratory},
  year = {1989},
  number = {FERMILAB-Pub-89/100-T},
  annote = {http://fnalpubs.fnal.gov/techpubs/1989preprints51100.html}
}

@ARTICLE{MADE89,
  author = {S.~Mader and V.~Kumar and H.~de Verneuil and P.~Chambon},
  title = {Three amino acids of the oestrogen receptor are essential to its
	ability to distinguish an oestrogen from a glucocorticoid-responsive
	element},
  journal = NAT,
  year = {1989},
  volume = {338},
  pages = {271--274},
  annote = {excellent for comparing sequences w/ others in the nuclear recp family,but
	major importance is that is says 3aa make diff betwn ER and GR}
}

@ARTICLE{MARQ89,
  author = {S. Marquesee and V. H. Robbins and R. L. Baldwin},
  title = {Unusually Stable Helix Formation in Short-Alanine Based Peptides},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1989},
  volume = {86},
  pages = {5286--5290}
}

@INCOLLECTION{MART89,
  author = {Thomas Martinetz and Helge Ritter and Klaus Schulten},
  title = {Kohonen's Self-Organizing Map for Modeling the Formation of the Auditory
	Cortex of a Bat},
  booktitle = {Connectionism in Perspective},
  publisher = {North-Holland},
  year = {1989},
  editor = {R. Pfeifer and Z. Schreter and F. Fogelman-Souli{\'e} and L. Steels},
  pages = {403--412},
  address = {Amsterdam}
}

@INPROCEEDINGS{MART89A,
  author = {Thomas Martinetz and Helge Ritter and Klaus Schulten},
  title = {{3D}-Neural-Net for Learning Visuomotor-Coordination of a Robot Arm},
  booktitle = {Proceedings of the International Joint Conference on Neural Networks,
	Washington},
  year = {1989},
  volume = {2},
  pages = {351--356},
  address = {San Diego},
  organization = {The Institute of Electrical and Electronics Engineers}
}

@ARTICLE{MAUZ89,
  author = {D. Mauzerall and N.L. Greenbaum},
  title = {The Absolute Size of A Photosynthetic Unit},
  journal = BBA,
  year = {1989},
  volume = {974},
  pages = {119--140}
}

@ARTICLE{MCIN89b,
  author = {T. J. Mcintosh and A.D. Magid and S. A. Simon},
  title = {Repulsive interactions between uncharged bilayers: hydration and
	fluctuation pressures for monoglycerides},
  journal = BJ,
  year = {1989},
  volume = {55},
  pages = {897--904}
}

@ARTICLE{MCIN89,
  author = {T. J. McIntosh and A. D. Magid and S. A. Simon},
  title = {Range of solvation pressure between lipid membranes: dependence on
	the packing density of solvent molecules},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {7904--7912}
}

@ARTICLE{MEND89,
  author = {Mendelsohn, R. and others},
  title = {Quantitative Determination of Conformational Disorder in the Acyl
	Chains of Phospholipid Bilayers by Infrared Spectroscopy},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {8934--8939},
  annote = {they find 3.6 gauche per lipid in the liquid phase},
  keywords = {DPPC; trans-gauche rotamers; experimental; membrane}
}

@ARTICLE{MEZE89,
  author = {Mihaly Mezei},
  title = {Evaluation of the Adaptive Umbrella Sampling Method},
  journal = MS,
  year = {1989},
  volume = {3},
  pages = {301--313},
  keywords = {free energy; {M}onte {C}arlo computer simulation; probability ratio
	method; adaptive umbrella sampling; alanine dipeptide}
}

@ARTICLE{MILL89,
  author = {K. D. Miller and J. B. Keller and M. P. Stryker},
  title = {Ocular Dominance Column Development: Analysis and Simulation},
  journal = SCI,
  year = {1989},
  volume = {245},
  pages = {605--615}
}

@ARTICLE{MINO89,
  author = {P.~D.~Minor and G.~Dunn and D.~M.~A.~Evans and D.~I.~Magrath and
	A.~John and J.~Howlett and A.~Phillips and G.~Westrop and K.~Wareham
	and J.~W.~Almond and J.~M.~Hogle},
  title = {The temperature-sensitivity of the sabin type 3 vaccine strain of
	poliovirus: molecular and structural effects of a mutation in the
	capsid protein VP3},
  journal = {J.~Gen.~Virol.},
  year = {1989},
  volume = {70},
  pages = {1177--1183}
}

@ARTICLE{MOBI89,
  author = {D. Mobilio and L.A. Marshall},
  title = {Recent advances in the design and evaluation of inhibitors of {PLA$_2$}},
  journal = {Ann. Rep. Med. Chem.},
  year = {1989},
  volume = {24},
  pages = {157--166},
  annote = {Drug Design}
}

@ARTICLE{MOGI89B,
  author = {T. Mogi and T. Marti and H. G. Khorana},
  title = {Structure-Function Studies on Bacteriorhodopsin .9. \ {S}ubstitution
	of Tryptophan Residues Affect Protein-Retinal Interactions in Bacteriorhodopsin},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {14197--14201}
}

@ARTICLE{MOGI89A,
  author = {T. Mogi and L. J. Stern and B. H. Chao and H. G. Khorana},
  title = {Structure-Function Studies on Bacteriorhodopsin .8. \ {S}ubstitution
	of the Membrane-Embedded {Proline}-50, {Proline}-91, and {Proline}-186\
	--\ The Effects are Determined by the Substituting Amino-Acids},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {14192--14196}
}

@ARTICLE{MONT89,
  author = {G. T. Montelione and H. A. Scheraga},
  title = {Formation of Local Structures in Protein Folding},
  journal = ACR,
  year = {1989},
  volume = {22},
  pages = {70--76}
}

@INBOOK{NATI89,
  pages = {201--205},
  title = {Opportunities in Biology},
  publisher = {National Academy Press},
  year = {1989},
  author = {{National Research Council}},
  address = {Washington}
}

@INCOLLECTION{NELS89,
  author = {M. E. Nelson and W. Furmanski and J. M. Bower},
  title = {Simulating Neurons and Networks on Parallel Computers},
  booktitle = {Methods in Neural Modeling: From Synapses to Networks},
  publisher = {MIT Press},
  year = {1989},
  editor = {C. Koch and I. Segev},
  pages = {397--437},
  address = {Cambridge}
}

@ARTICLE{OlEl96,
  author = {R. Olender and R. Elber},
  title = {Calculation of classical trajectories with a very large time step:
	Formalism and numerical examples},
  journal = JCP,
  year = {1989},
  volume = {105},
  pages = {9299--9315},
  number = {20}
}

@ARTICLE{OTTO89,
  author = {Michael Ottolenghi and Mordechai Sheves},
  title = {Synthetic Retinals as Probes for the Binding Site and Photoreactions
	in Rhodopsins},
  journal = JMEB,
  year = {1989},
  volume = {112},
  pages = {193--212}
}

@ARTICLE{PAI89,
  author = {E. F. Pai and W. Kabsch and U. Krengel and K. C. Holmes and J. John
	and A. Wittinghofer},
  title = {Structure of the guanine-nucleotide-binding domain of the {Ha}-ras
	oncogene product p21 in the triphosphate conformation},
  journal = NAT,
  year = {1989},
  volume = {341},
  pages = {209--214}
}

@ARTICLE{PeSc89,
  author = {C. S. Peskin and T. Schlick},
  title = {Molecular dynamics by the backward {E}uler method},
  journal = {Comm.\ Pure and Appl.\ Math.},
  year = {1989},
  volume = {42},
  pages = {1001--1031}
}

@ARTICLE{PESK89,
  author = {C. S. Peskin and T. Schlick},
  title = {Molecular dynamics by the backward {E}uler method},
  journal = {Comm.\ Pure and Appl.\ Math.},
  year = {1989},
  volume = {42},
  pages = {1001--1031}
}

@ARTICLE{PETE89,
  author = {C. Peterson and B. S{\"o}derberg},
  title = {A New Method for mapping Optimization Problems onto Neural Neural
	Networks},
  journal = {Int. Journ. of Neural Syst.},
  year = {1989},
  volume = {1},
  pages = {3--22}
}

@ARTICLE{PFEI89,
  author = {W. Pfeiffer and Th. Henkel and Erich Sackmann and W. Knoll and D.
	Richter},
  title = {Local Dynamics of Lipid Bilayers Studied by Incoherent Quasi-Elastic
	Neutron Scattering},
  journal = EPL,
  year = {1989},
  volume = {8},
  pages = {201--206},
  number = {2},
  annote = {D_lat=0.02 * 10^-5 cm^2/s; D_tr=0.24 * 10^-5 cm^2/s; D_rot=5.6*10^10/s;
	jump frq. \tau = 10^8/s...2.3*10^7/s; also has values for gel phase},
  keywords = {experimental; membrane; diffusion; DPPC; LC phase; gel phase},
  suggestions = {compare diffusion constants; compare rotational motion; do we see
	a head group flip?}
}

@ARTICLE{PIDG89,
  author = {C. Pidgeon},
  title = {Immobilized Artificial Membrane Chromatography: Supports Composed
	of Membrane Lipids},
  journal = {Anal.\/Biochem.\/},
  year = {1989},
  volume = {176},
  pages = {36},
  annote = {experimental}
}

@ARTICLE{PiKS89,
  author = {L. Piela and J. Kostrowicki and H. A. Scheraga},
  title = {The Multiple Minima Problem in the Conformational Analysis of Molecules:
	Deformation of the Protein Energy Hypersurface by the Diffusion Equation
	Method},
  journal = {J. Phys.\ Chem.},
  year = {1989},
  volume = {93},
  pages = {3339--3346}
}

@ARTICLE{POLL89,
  author = {W. T. Pollard and C. H. {Brito Cruz} and C. V. Shank and R. A. Mathies},
  title = {Direct Observation of the Excited-State {\it cis-trans} Photoisomerization
	of Bacteriorhodopsin: Multilevel Line Shape Theory for Femtosecond
	Dynamic Hole Burning and Its Application},
  journal = JCP,
  year = {1989},
  volume = {90},
  pages = {199--208}
}

@ARTICLE{POST89,
  author = {C.~B.~Post and C.~M.~Dobson and M.~Karplus},
  title = {A molecular dynamics analysis of protein structural elements.},
  journal = PSFG,
  year = {1989},
  volume = {5},
  pages = {337--354}
}

@ARTICLE{Qin89,
  author = {M.-Z. Qin},
  title = {Canonical Difference Scheme for the \mbox{Hamiltonian} Equation},
  journal = {Mathematical Methods in the Applied Sciences},
  year = {1989},
  volume = {11},
  pages = {543--557}
}

@UNPUBLISHED{QiZh89,
  author = {M.-Z. Qin and M.-Q. Zhang},
  title = {Symplectic \mbox{Runge-Kutta} schemes for \mbox{Hamiltonian} systems},
  note = {Preprint},
  year = {1989}
}

@ARTICLE{FINC89,
  author = {A. R. C. Raine and David Fincham and W. Smith},
  title = {Systolic Loop Methods for Molecular Dynamics Simualtion Using Multiple
	Transputers},
  journal = CPC,
  year = {1989},
  volume = {55},
  pages = {13--30}
}

@ARTICLE{RAND89,
  author = {R. P. Rand and V. A. Parsegian},
  title = {Hydration forces between phospholipid bilayers},
  journal = BBA,
  year = {1989},
  volume = {988},
  pages = {351--376},
  annote = {requested Tx=19920908., surface area per lipid 68--71\AA^2}
}

@ARTICLE{RAVI89,
  author = {G.~Ravishanker and S.~Swaminathan and D.~L.~Beveridge and R.~Lavery
	and H.~Sklenar},
  title = {Conformational and helicoidal analysis of 30 ps of molecular dynamics
	on the d({CGCGAATTCGCG}) double helix.},
  journal = {J.\ Biomol.\ Str.\ Dyn.},
  year = {1989},
  volume = {6},
  pages = {669--699},
  number = {4},
  annonte = {use as reference to MDtoolchest when producing graphics either pro
	or DNA},
  keywords = {MD Toolchest, Dials and Windows}
}

@BOOK{Risk89,
  title = {The {F}okker-{P}lanck Equation},
  publisher = {Springer-Verlag},
  year = {1989},
  author = {H. Risken},
  address = {Berlin},
  edition = {2nd}
}

@ARTICLE{RITT89,
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  title = {Wie neuronale {N}etzwerke {R}oboter steuern k\"onnen},
  journal = MCM,
  year = {1989},
  volume = {2},
  pages = {48--61}
}

@ARTICLE{RITT89A,
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  title = {Topology-Conserving Maps for Learning Visuo-motor-Coordination},
  journal = NNET,
  year = {1989},
  volume = {2},
  pages = {159--168}
}

@INCOLLECTION{RITT89B,
  author = {Helge Ritter and Thomas Martinetz and Klaus Schulten},
  title = {Topology-Conserving Maps for Motor Control},
  booktitle = {Neural Networks: From Models to Applications, {N'EURO~'88}},
  publisher = {{EZIDET}},
  year = {1989},
  editor = {L. Personnaz and G. Dreyfus},
  pages = {579--591},
  address = {Paris}
}

@ARTICLE{RODG89,
  author = {P. Mark Rodger},
  title = {On the Accuracy of some Common Molecular Dynamics Algorithms},
  journal = MS,
  year = {1989},
  volume = {3},
  pages = {263--269},
  annote = {Comparision of integration schemes concerning accuracy. Very critical
	(mathematical), describes Verlet-equivalence, Beeman. Very good article.}
}

@ARTICLE{ROTH89,
  author = {K. J. Rothschild and M. S. Braiman and T. Mogi and L. J. Stern and
	H. G. Khorana},
  title = {Conserved Amino Acids in F-Helix of Bacteriorhodopsin Form Part of
	a Retinal Binding Pocket},
  journal = FEBS,
  year = {1989},
  volume = {250},
  pages = {448--452}
}

@ARTICLE{RUBN89,
  author = {Jeanne Rubner and Klaus Schulten},
  title = {A Regularized Approach to Color Constancy},
  journal = BC,
  year = {1989},
  volume = {61},
  pages = {29--36}
}

@INCOLLECTION{SAFI89,
  author = {S. Safinya},
  title = {Rigid and fluctuating surfaces: A series of synchrotron x-ray scattering
	studies of interacting stacked membranes},
  booktitle = {Phase Transitions in Soft Condensed Matter},
  publisher = {Plenum Publishing Corp.},
  year = {1989},
  editor = {T. Riste and D. Sherrington},
  pages = {249--270},
  address = {New York},
  annote = {requested Tx=19920908.; at binding}
}

@ARTICLE{SCHE89,
  author = {M.~Schena and L.~P.~Freedman and K.~R.~Yamamoto},
  title = {Mutations in the glucocorticoid receptor zinc finger region that
	distinguish interdigitated {DNA} binding and transcriptional enhancement
	activities},
  journal = {Genes and Development},
  year = {1989},
  volume = {3},
  pages = {1590--1601},
  annote = {original location of the DBD}
}

@ARTICLE{SCHE89A,
  author = {P. Scherrer and M. Matthew and W. Sperling and W. Stoeckenius},
  title = {Retinal isomer ratio in dark-adapted purple membrane and bacteriorhodopsin
	monomer.},
  journal = BCH,
  year = {1989},
  volume = {26},
  pages = {829--834}
}

@ARTICLE{SCHN89,
  author = {G.~Schneider and R.~Diller and M.~Stockburger},
  title = {Photochemical quantum yield of bacteriorhodopsin from resonance {Raman}
	scattering as a probe for photolysis},
  journal = CP,
  year = {1989},
  volume = {131},
  pages = {17--29}
}

@ARTICLE{SCHW89,
  author = {R. A. Schwendener and R. {W{\"u}thrich} and S. Duewell and G. Westera
	and G. K. von Schulthess},
  title = {Small unilaminar liposomes as {MR} contrast agents loaded with paramagnetic
	{Mn}-, {Gd}- and {Fe-DTPA}-stearate complexes},
  journal = {International Journal of Pharmazeutics},
  year = {1989},
  volume = {{\bf 49}},
  pages = {249--259},
  keywords = {liposomes, Gd-DTPA}
}

@ARTICLE{SCOT89,
  author = {H.L. Scot and S. Kalaskar},
  title = {Lipid chains and cholesterol in model membranes: a {M}onte {C}arlo
	study},
  journal = BCH,
  year = {1989},
  volume = {328},
  pages = {3687--3691}
}

@UNPUBLISHED{SCOV89,
  author = {C. Scovel},
  title = {Symplectic Numerical Integration of {Hamiltonian} Systems},
  note = {manuscript},
  year = {1989}
}

@ARTICLE{SEEH89,
  author = {S. H. Seeholzer and A. J. Wand},
  title = {Structual Characterization of the Interactions Between Calmodulin
	and Skeltal Muscle Myosin Light Chain Kinase: Effect of Peptide (576-594)G
	Binding on the {Ca$^{2+}$}-Binding Domains},
  journal = {Biochemistry},
  year = {1989},
  volume = {28},
  pages = {4011--4020}
}

@ARTICLE{SEEL89,
  author = {Joachim Seelig},
  title = {Lipid Protein Interactions in Biological Membranes},
  journal = BMN,
  year = {1989},
  volume = {195},
  pages = {105--114},
  editor = {C. L. L{\'e}ger and G. B{\'e}r{\'e}ziat},
  keywords = {melittin; membrane; lipid-protein interaction; POPC; headgroup orientation}
}

@ARTICLE{SENS89,
  author = {Sension, R J and Hudson, B S},
  title = {Vacuum ultraviolet resonance {Raman} studies of the excited electronic
	states of ethylene},
  journal = {J. Chem. Phys.},
  year = {1989},
  volume = {90},
  pages = {1377--1389}
}

@ARTICLE{SIMO89,
  author = {S. A. Simon and T. J. Mcintosh},
  title = {Magnitude of the solvation presuure depends on dipole potential},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {9263--9267},
  annote = {Hydration pressure of certain lipids prove to be proportional to
	the square of dipole potential. Suggest both of these quantities
	decay exponentially outside of bilayer edge with a decay length of
	1-2 {\AA\ } in water. Formamide and 1,3-propanediol decrease the
	dipole potential. On monolayer dipole potential measured is about
	400mV, larger than bilayer, reason unkonwn but can be due to difference
	of the method. Cholestrol has also similar potential. Suggest: calculate
	hydration force using our model. Good reference listed.}
}

@ARTICLE{SKLE89,
  author = {H.~Sklenar and C.~Etchebest and R.~Lavery},
  title = {The definition of generalized helicoidal parameters and of axis of
	curvature for irregular nucleic acids.},
  journal = {Proteins: Structure, Function Genet.},
  year = {1989},
  volume = {6},
  pages = {46--60},
  annote = {use as reference to MDtoolchest if analyzed protein, add RAVI89 also}
}

@ARTICLE{SMAL89,
  author = {J. V. Small},
  title = {Microfilament-based motility in non-muscle cells},
  journal = COCB,
  year = {1989},
  volume = {1},
  pages = {75--79}
}

@ARTICLE{SMIT89,
  author = {S. O. Smith and H. J. M. {de Groot} and R. Gebhard and J. M. L. Courtin
	and J. Lugtenburg and J. Herzfeld and R. G. Griffin},
  title = {Structure and Protein Environment of the Retinal Chromophore in Light-
	and Dark-Adapted Bacteriorhdopsin Studied by Solid-State {NMR}},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {8897--8904}
}

@ARTICLE{SOPP89,
  author = {J. Soppa and J. Otomo and L. Straub and J. Tittor and S. Messen and
	D. Oesterhelt},
  title = {Bacteriorhodopsin Mutants of Halobacterium {sp. GRB.} Characterization
	of Mutants},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {13049--13056}
}

@ARTICLE{SPER89,
  author = {M.M. Sperotto and J.H. Ipsen and O.G. Mouritsen},
  title = {Theory of protein--induced lateral phase separation in lipid membranes},
  journal = {Cell Biophysics},
  year = {1989},
  volume = {14},
  pages = {79--95}
}

@ARTICLE{SPEY89,
  author = {J. Speyer and R. Weber and S. Das Gupta and R. Griffin},
  title = {Anistropic $^2$H {NMR} spin-lattice relaxation in C$_{\alpha}$-phase
	cerebroside bilayers},
  journal = BCH,
  year = {1989},
  volume = {28},
  pages = {9569--9574}
}

@ARTICLE{STEI89,
  author = {U.E. Steiner and T. Ulrich},
  title = {Magnetic field effects in chemical kinetics and related phenomena},
  journal = {Chem.~Rev.},
  year = {1989},
  volume = {89},
  pages = {51--147}
}

@ARTICLE{STER89,
  author = {L. J. Stern and H. G. Khorana},
  title = {Structure-Function Studies on Bacteriorhodopsin. {I}ndividual Substitutions
	of Arginine Residues by Glutamine Affect Chromophore Formation, Photocycle,
	and Proton Translocation},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {14202--14208}
}

@ARTICLE{StHa89,
  author = {C. S. Strom and P. Hartman},
  title = {Comparison between {G}aussian and exponential charge-distributions
	in {E}wald surface-potentials and fields},
  journal = {Acta Crystalographica section A},
  year = {1989},
  volume = {45},
  pages = {371--380}
}

@INCOLLECTION{SUBR89,
  author = {Subramaniam, S. and McCammon, J. A. and Bacquet, R. J.},
  title = {Protein Stability},
  booktitle = {The Immune Response to Structurally Defined Proteins: The Lysozyme
	Model},
  publisher = {Adenine Press},
  year = {1989},
  editor = {S. Smith-Gill and E. Sercarz},
  address = {New York}
}

@ARTICLE{SUMM89,
  author = {Neena L. Summers and Martin Karplus},
  title = {Construction of side-chains in homology modelling. {Application}
	to the {C-terminal} lobe of {R}hizopuspepsin},
  journal = JMB,
  year = {1989},
  volume = {210},
  pages = {785--811}
}

@ARTICLE{Suri89,
  author = {Y. B. Suris},
  title = {The canonicity of Mappings Generated by \mbox{Runge-Kutta} Type Methods
	When Integrating the System $\ddot{x} = \frac{-\partial U}{\partial
	x}$},
  journal = {Zh. Vychisl. Mat. i Mat. Fiz.},
  year = {1989},
  volume = {29},
  pages = {202--211},
  note = {(in Russian). Same as {\em U.S.S.R. Comput. Maths. Phys.,} 29(1):138-144,
	1989}
}

@ARTICLE{TAYL89,
  author = {William R. Taylor and Christine A. Orango},
  title = {Protein Structure Alignment},
  journal = JMB,
  year = {1989},
  volume = {208},
  pages = {1--22}
}

@ARTICLE{ThMK89,
  author = {D. Thirumalai and R. D. Mountain and T. R. Kirkpatrick},
  title = {Ergodic Behavior in Supercooled Liquids and in Glasses},
  journal = PRA,
  year = {1989},
  volume = {39},
  pages = {3563}
}

@ARTICLE{TILC89,
  author = {C. Tilcock and E. Unger and P. Cullis and P. MacDougall},
  title = {Liposomal {Gd-DTPA}: Preparation and Characterization of Relaxivity},
  journal = {Radiology},
  year = {1989},
  volume = {{\bf 171}},
  pages = {77--80},
  keywords = {paramagnetic}
}

@BOOK{Toda89,
  title = {Nonlinear Waves and Solitons},
  publisher = {Kluwer Academic Publisher},
  year = {1989},
  author = {M. Toda}
}

@ARTICLE{TOMA89,
  author = {A.G. Tomasselli and J. Hui and J. Fisher and H. Z.-Neely and I.M.
	Reardon and E. Oriaku and F.J. K{\'e}zdy and R.L. Heinrikson},
  title = {Dimerization and activation of porcine pancreatic phospholipase {A$_2$}
	via substrate level acylation of Lysine 56},
  journal = JBC,
  year = {1989},
  volume = {17},
  pages = {10041--10047}
}

@ARTICLE{TSAI89,
  author = {S.~Y.~Tsai and M.~Tsai and B.~W.~O'Malley},
  title = {Cooperative Binding of Steroid Hormone Receptors Contributes to Transcriptional
	Synergism at Target Enhancer Elements},
  journal = {Cell},
  year = {1989},
  volume = {57},
  pages = {443--448},
  annote = {says bind cooperatively, same as ERIK90,WRIG90,WRIG91a}
}

@ARTICLE{UMES89,
  author = {K.~Umesono and R.~M.~Evans},
  title = {Determinants of target gene specificity for steroid/thyroid hormone
	receptors},
  journal = {Cell},
  year = {1989},
  volume = {57},
  pages = {1139--1146},
  annote = {pathway of evolution from diffs in sequence and binding of GR/ER/TR}
}

@ARTICLE{UNGE89,
  author = {E. C. Unger and T. Winokur and others},
  title = {Hepatic Metastases: Liposomal {Gd-DTPA-enhanced MR Imaging}},
  journal = {Radiology},
  year = {1989},
  volume = {{\bf 171}},
  pages = {81--85},
  keywords = {liver, paramagnetic}
}

@ARTICLE{VALE89,
  author = {Catherine Valentin-Ranc and Marie-France Carlier},
  title = {Evidence for the Direct Interaction between Tightly Bound Divalent
	Metal Ion and {ATP} on Actin},
  journal = JBC,
  year = {1989},
  volume = {264},
  pages = {20871--20880}
}

@ARTICLE{VIGN89,
  author = {M.~L.~Vignais and A.~Sentenac},
  title = {Asymmetric {\sc DNA} bending induced by the yeast multifunctional
	factor {\sc TUF}.},
  journal = {J. Biol. Chem.},
  year = {1989},
  volume = {264},
  pages = {8463--8625},
  annote = {not read, taken from anne's paper, eukaryotic system}
}

@ARTICLE{VISS89,
  author = {K.J. Visscher and H. Bergstrom and V. Sundstrom and C.N. Hunter and
	R. {van Grondelle}},
  title = {Temperature Dependence of Energy Transfer from the Long Wavelength
	Antenna BChl-896 to the Reaction Center in {\em Rhodospirillum Rubrum},
	{\em Rhodobacter Sphaeroides} (w.t. and M21 Mutant) from 77 to 177
	K, Studied by Picosecond Absorption Spectroscopy},
  journal = {Photosynthesis Research },
  year = {1989},
  volume = {22},
  pages = {211--217}
}

@ARTICLE{WAND89,
  author = {A. J. Wand and D. L. DiStefano and Y. Feng and H. Roder and S. W.
	Englander},
  title = {Proton Resonance Assignments of Horse Ferrocytochrome~C},
  journal = {Biochemistry},
  year = {1989},
  volume = {28},
  pages = {186--194}
}

@ARTICLE{ChGS89,
  author = {George Wang and Wayne C. Guida and W. Clark Still},
  title = {Fast {E}wald sums for general van der {W}aals potentials},
  journal = {J. Am. Chem. Soc.},
  year = {1989},
  volume = {111},
  pages = {4379--4386}
}

@ARTICLE{WARS89,
  author = {A. Warshel and Z. T. Chu and W. W. Parson},
  title = {Dispersed Polaron Simulations of Electron Transfer in Photosynthetic
	Reaction Center},
  journal = SCI,
  year = {1989},
  volume = {246},
  pages = {112--116}
}

@INCOLLECTION{WEHM89,
  author = {U. Wehmeier and D. Dong and C. Koch and D. van Essen},
  title = {Modeling the Mammalian Visual System},
  booktitle = {Methods in Neuronal Modeling},
  publisher = {MIT Press},
  year = {1989},
  editor = {C. Koch and I. Segev},
  pages = {335--359}
}

@ARTICLE{WEND89,
  author = {J. J. Wendoloski and S. J. Kimatian and C. E. Schutt and F. R. Salemme},
  title = {Molecular Dynamics Simulation of a Phospholipid Micelle},
  journal = SCI,
  year = {1989},
  volume = {243},
  pages = {636--638},
  annote = {85~LPE and 1591 water molecules; 125\,ps simulation; },
  keywords = {lysophosphatidylethanolamin; polymorphic transition; micelle}
}

@ARTICLE{WEST89,
  author = {G.~D.~Westrop and K.~A.~Wareham and D.~M.~A.~Evans and G.~Dunn and
	P.~D.~Minor and D.~I.~Magrath and F.~Taffs and S.~Marsden and M.~A.~Skinner
	and G.~C.~Schild and J.~W.~Almond},
  title = {Genetic basis of attenuation of the Sabin type 3 oral poliovirus
	vaccine},
  journal = {J.~Virol.},
  year = {1989},
  volume = {63},
  pages = {1338--1344}
}

@ARTICLE{WILC89,
  author = {M. Wilcheck and E. A. Bayer},
  title = {Avidin-Biotin Technology Ten Years On: {H}as It Lived Up To Its Expectation?},
  journal = TIBS,
  year = {1989},
  volume = {14},
  pages = {408--412},
  annote = {june 1}
}

@ARTICLE{WILS89,
  author = {M. A. Wilson and U. S. Bhalla and J. D. Uhley and J. M. Bower},
  title = {GENESIS: A System for simulating neural networks},
  journal = {Advances in Neural Information Processing Systems},
  year = {1989},
  pages = {485--492},
  address = {San Mateo, CA},
  editor = {D. Touretzky},
  publisher = {Morgan-Kaufmann}
}

@ARTICLE{WONG89,
  author = {C. F. Wong and C. Zheng and J. A. McCammon},
  title = {Glass transition in {SPC}/{E} water and in protein solution: A molecular
	dynamics simulation study},
  journal = CPL,
  year = {1989},
  volume = {154},
  pages = {151--154}
}

@ARTICLE{YAN89,
  author = {J.~C. Yan and S.~F. Lundstrom},
  title = {The `Post-Game Analysis' Framework --- Developing Resource Management
	Strategies for Concurrent Systems},
  journal = {IEEE Transactions on Knowledge and Data Engineering},
  year = {1989},
  volume = {1},
  pages = {293--309},
  number = {3},
  keywords = {distributed systems; parallel processing; performance evaluation;
	resource management; rule-based conflict resolution; task allocation
	algorithm}
}

@ARTICLE{YIP89,
  author = {P. Yip and D. A. Case},
  title = {A New Method for Refinement of Macromolecular Structures Based on
	Nuclear {O}verhauser Effect Spectra},
  journal = JMR,
  year = {1989},
  volume = {83},
  pages = {643--648}
}

@TECHREPORT{ZHAO89,
  author = {F. Zhao and S. L. Johnsson},
  title = {The parallel multipole method on the Connection Machine},
  institution = {Rept. YALEU/DCS/RR-749},
  year = {1989}
}

@ARTICLE{ZHEN89,
  author = {Chong Zheng and J. Andrew McCammon and Peter G. Wolynes},
  title = {Quantum Simulation of Nuclear Rearrangement in Electron Transfer
	Reactions},
  journal = PNAS,
  year = {1989},
  volume = {86},
  pages = {6441--6444}
}

@ARTICLE{ZHOU89,
  author = {Z. Zhou and Clint Potter and Paul Lauterbur and B. Voth},
  title = {3D Microscopic NMR Imaging with (6.37$\mu$m)$^3$ Isotropic Resolution},
  journal = {Abstracts, 8th Annual Meeting SMRM},
  year = {1989},
  pages = {286},
  address = {Amsterdam}
}

@ARTICLE{ZUKE89,
  author = {M. Zuker and R. L. Somorjai},
  title = {The Alignment of Protein Structures in Three Dimensions},
  journal = BMB,
  year = {1989},
  volume = {51},
  pages = {55--78}
}

@ARTICLE{ZWIE89,
  author = {C.~Zwieb and J.~Kim and S. Adhya},
  title = {{\sc DNA} bending by negative regulatory proteins: gal and lac repressors.},
  journal = {Genes and Development},
  year = {1989},
  volume = {3},
  pages = {606--611},
  annote = {not read cited in anne's paper, procaryotic sytem, also has cro which
	does NOT bend dna}
}

@PHDTHESIS{Shen88,
  author = {Qin Sheng},
  title = {Solving Partial Differential Equations by Exponential Splitting},
  school = {King's College, Cambridge},
  year = {1988},
  month = OCT
}

@MASTERSTHESIS{WIND88,
  author = {Andreas Windemuth},
  title = {{D}ynamiksimulation von {M}akromolek\"ulen},
  school = {{T}echnical {U}niversity of {M}unich, {P}hysics Department, T~30},
  year = {1988},
  address = {James-Franck-Street, D-8046~Garching / Munich},
  month = AUG
}

@INPROCEEDINGS{CARR88,
  author = {Nicholas Carriero and David Gelernter},
  title = {Applications Experience with Linda},
  booktitle = {Proceedings of the {ACM/SIGPLAN PPELS} 1988: parallel programming:
	experience with applications, languages, and systems},
  year = {1988},
  volume = {23},
  number = {9},
  pages = {173--187},
  address = {New York},
  month = JUL,
  publisher = {ACM press},
  note = {ACM = Association for Computing Machinery}
}

@INPROCEEDINGS{OUH-88,
  author = {Ouh-young, M. and Pique, M. and Hughes, J. and Srinivasan, N. and
	Brooks, F.},
  title = {Using a Manipulator For Force Display in Molecular Docking},
  booktitle = {Proc.\ of the {IEEE} Robotics and Automation Conference~3},
  year = {1988},
  pages = {1824--1829},
  month = APR
}

@INCOLLECTION{GRON88,
  author = {R. {van Grondelle} and V. Sundstrom},
  title = {Excitation energy transfer in photosynthesis},
  booktitle = {Photosynthetic Light--Harvesting Systems},
  publisher = {Walter de Gruyter \& Co.},
  year = {1988},
  editor = {H. Scheer},
  pages = {403--438},
  address = {Berlin, New York}
}

@ARTICLE{AbMa88,
  author = {R. A. Abagyan and V. N. Maiorov},
  title = {A Simple Qualitative Representation of Polypeptide Chain Folds: Comparison
	of Protein Tertiary Structures},
  journal = JBSD,
  year = {1988},
  volume = {5},
  pages = {1267--1279}
}

@ARTICLE{Agga88,
  author = {A. K. Aggarwal and D. W. Rodgers and M. Drottar and M. Ptashne and
	S. C. Harrison},
  title = {Recognition of a {DNA} Operator by the Repressor of Phage~434: A
	View at High Resolution},
  journal = SCI,
  year = {1988},
  volume = {242},
  pages = {899--907}
}

@ARTICLE{ANDE88,
  author = {A. G. Anderson and J. Hermans},
  title = {Microfolding: Conformational Probability Map for the Alanine Dipeptide
	in Water From Molecular Dynamics Simulations},
  journal = PSFG,
  year = {1988},
  volume = {3},
  pages = {262--265}
}

@BOOK{Arno88,
  title = {Geometrical Methods in the Theory of Ordinary Differential Equations},
  publisher = {Springer-Verlag},
  year = {1988},
  author = {V. I. {Arnol'd}},
  address = {New York}
}

@ARTICLE{ANGE88,
  author = {B. G. Ang\,eniol and de La Croix Vaubois and J. Y. Le Texier},
  title = {Self-Organizizing Feature Maps and the Travelling Salesman Problem},
  journal = {Neural Networks},
  year = {1988},
  volume = {1},
  pages = {289--293}
}

@ARTICLE{BABU88,
  author = {Y. Sudhakar Babu and Charles E. Bugg and William J. Cook},
  title = {Structure of Calmodulin Refined at 2.2\,{{\AA}} Resolution},
  journal = JMB,
  year = {1988},
  volume = {204},
  pages = {191--204}
}

@ARTICLE{BACI88,
  author = {G. Bacic and M. R. Niesman and H. F. Bennett and R. L. Magin and
	H. M. Swartz},
  title = {{Modulation of Water Proton Relaxation Rates by Liposomes Containing
	Paramagnetic Materials}},
  journal = mrm,
  year = {1988},
  volume = {{\bf 6}},
  brief = {Mentions that liposome permeabilities vary by two orders of magnitude
	due to composition alone.},
  keywords = {paramagnetic contrast agent}
}

@ARTICLE{BAE88,
  author = {Bae, D.-S. and Haug, E. J.},
  title = {A recursive formulation for constrained mechanical system dynamics:
	Part {II}. Closed loop systems},
  journal = {Mech. Struct. \& Mach.},
  year = {1988},
  volume = {15},
  pages = {481--506}
}

@ARTICLE{BALA88,
  author = {S. P. Balashov and F. F. Litvin and V. A. Sineshchekov},
  title = {Photochemical Processes of Light Energy Transformation in Bacteriorhodopsin},
  journal = SSRSD,
  year = {1988},
  volume = {8},
  pages = {1--61}
}

@ARTICLE{BARL88,
  author = {P. N. Barlow and J.-C. Vidal and M. D. Lister and E. A. Dennis and
	P. B. Sigler},
  title = {Probing the role of substrate conformation in phospholipase {A$_2$}
	action on aggregated phospholipids using constrained phosphotidylcholine
	analogues},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {12954--12963},
  annote = {substrate conformation}
}

@ARTICLE{BART88,
  author = {Geoffrey J. Barton and Michael J. E. Sternberg},
  title = {{LOPAL} and {SCAMP}: techniques for the comparison and display of
	protein structures},
  journal = JMG,
  year = {1988},
  volume = {6},
  pages = {190--196}
}

@ARTICLE{BASH88,
  author = {D. Bashford and F. E. Cohen and M. Karplus and I. D. Kuntz and D.
	L. Weaver},
  title = {Diffusion-Collision Model for the Folding Kinetics of Myoglobin},
  journal = PSFG,
  year = {1988},
  volume = {4},
  pages = {211--227}
}

@ARTICLE{BAUE88,
  author = {Hans-Ulrich Bauer and Walter Nadler and Klaus Schulten},
  title = {Generalized Moment Expansion of Dynamic Correlation Functions in
	Finite {I}sing Systems},
  journal = PRB,
  year = {1988},
  volume = {38},
  pages = {445--458}
}

@ARTICLE{BEN85,
  author = {A. Ben-Shaul and I. Szleifer and W.M. Gelbart},
  title = {Chain organization and thermodynamics in micelles and bilayers},
  journal = JCP,
  year = {1988},
  volume = {83},
  pages = {3597--3611}
}

@ARTICLE{BicZ88,
  author = {D.~Bicout and A.~Szabo},
  title = {Electron transfer reaction dynamics in non-{D}ebye solvents},
  journal = JCP,
  year = {1988},
  volume = {109},
  pages = {2325--2338},
  number = {6}
}

@ARTICLE{BITT88,
  author = {Robert Bittl and Klaus Schulten},
  title = {Length Dependence of the Magnetic Field Modulated Triplet Yield of
	Photogenerated Biradicals},
  journal = CPL,
  year = {1988},
  volume = {146},
  pages = {58--62}
}

@ARTICLE{BOEH88,
  author = {Klaus Boehncke and Christoph K{\"o}hler and Georg Meyer-Berg and
	Klaus Schulten},
  title = {Eine {C}omputersimulation k\"unstlicher {W}esen --- {E}xperimente
	in einer Welt synthetischer {P}sychologie},
  journal = MCM,
  year = {1988},
  volume = {7},
  pages = {34--48}
}

@ARTICLE{BORG88,
  author = {B. A. Borgias and T. L. James},
  title = {{COMATOSE}: {A} Method for Constrained Refinement of Macromolecular
	Structure Based on Two Dimensional Nuclear {O}verhauser Effect Spectra},
  journal = JMR,
  year = {1988},
  volume = {79},
  pages = {493--512}
}

@ARTICLE{BOWE88,
  author = {J. M. Bower and M. E. Nelson and M. A. Wilsonand G. C. Fox and W.
	Furmanski},
  title = {Piriform (Olfactory) Cortex Model on the Hypercube},
  journal = {Third Conference on Hypercube Concurrent Computers and Applications},
  year = {1988},
  pages = {977--987},
  address = {New York},
  editor = {G. Fox}
}

@ARTICLE{BRAA88,
  author = {V. L. B. Braach-Maksvytis and B. A. Cornell},
  title = {Chemical shift anisotropies obtained from aligned egg yolk phosphatidylcholine
	by solid-state {$^13$C} nuclear magnetic resonance},
  journal = BJ,
  year = {1988},
  volume = {53},
  pages = {839--843},
  annote = {requested Tx=19921106.}
}

@ARTICLE{BRAI88,
  author = {M. S. Braiman and T. Mogi and T. Marti and L. J. Stern and H. G.
	Khorana and K. J. Rothschild},
  title = {Vibrational Spectroscopy of Bacteriorhodopsin Mutants: Light-Driven
	Proton Transport Involves Protonation Changes of Aspartic Acid Residues
	85, 96, and 212},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {8516--8520}
}

@BOOK{BrKP88,
  title = {Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics},
  publisher = {John Wiley and Sons},
  year = {1988},
  author = {C. L. {Brooks III} and M. Karplus and B. M. Pettitt}
}

@BOOK{BROO88,
  title = {Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics},
  publisher = {John Wiley and Sons},
  year = {1988},
  author = {Charles L. {Brooks~I{}I{}I} and M. Karplus and B. M. Pettitt},
  volume = {LXXI},
  series = {Advances in Chemical Physics},
  address = {New York}
}

@ARTICLE{BRUG88,
  author = {F. Brug{\`e} and V. Martorana and S. L. Fornili},
  title = {Concurrent Molecular Dynamics Simulation of {ST2} Water on a Transputer
	Array},
  journal = MS,
  year = {1988},
  volume = {1},
  pages = {309--320},
  annote = {SHAKE is mentioned but not explained},
  keywords = {Transputer (T414); MIMD; multiprocessor system; processor array; concurrent
	water simulation; parallelism; ST2-water; SHAKE; boustrophedonic
	particle mapping}
}

@UNPUBLISHED{Brun88,
  author = {A. T. Br{\"u}nger},
  title = {\mbox{X-PLOR}},
  note = {Dept. of Molecular Biophysics and Biochemistry, Yale Univ., New Haven,
	Conn},
  year = {1988}
}

@MANUAL{BRUN88A,
  title = {{X-PLOR}},
  author = {Axel T. Br{\"u}nger},
  organization = {The Howard Hughes Medical Institute and Department of Molecular Biophysics
	and Biochemistry, Yale University},
  address = {New Haven, CT},
  year = {1988}
}

@INCOLLECTION{BUHM88,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Storing Sequences of Biased Patterns in Neural Networks with Stochastic
	Dynamics},
  booktitle = {Neural Computers},
  publisher = {Springer},
  year = {1988},
  editor = {R. Eckmiller and Ch. von der Malsburg},
  series = {Computer and Systems Sciences},
  pages = {231--242}
}

@INPROCEEDINGS{BUHM88A,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Invariant Pattern Recognition by Means of Fast Synaptic Plasticity},
  booktitle = {IEEE International Conference on Neural Networks, San Diego, California,
	July 24--27, 1988},
  year = {1988},
  volume = {1},
  pages = {125--132},
  address = {New York},
  publisher = {The Institute of Electrical and Electronics Engineers}
}

@ARTICLE{BYLI88,
  author = {E.J. Bylina and S.J. Robles and D.C. Youvan},
  title = {Directed Mutations Affecting the Putative Bacteriochlorophyll-Binding
	Sites in the Light-Harvesting {I} Antenna of {{\em {R}hodobacter
	capsulatus}}},
  journal = {Israel Journal of Chemistry},
  year = {1988},
  volume = {28},
  pages = {73}
}

@ARTICLE{CaPa88,
  author = {R. Car and M. Parrinello},
  title = {Structural, Dynamics and Electronic Properties of Amorphous Silicon,
	an Ab Initio Molecular-Dynamics Study},
  journal = {Phys. Rev. Lett.},
  year = {1988},
  volume = {60},
  pages = {204--207}
}

@ARTICLE{CARL88,
  author = {M.-F. Carlier and D. Pantaloni},
  title = {Binding of Phosphate to {F-ADP}-actin and Role of {F-ADP-P$_i$}-actin
	in {ATP}-actin Polymerization},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {817--825}
}

@ARTICLE{CJGE88,
  author = {C.-H. Chang and R. Jonas and R. Govindjee and T.G. Ebrey},
  title = {Regeneration of Blue and Purple Membranes for Deionized Bleached
	Membranes of {\it {H}alobacterium halobium}},
  journal = PCPB,
  year = {1988},
  volume = {47},
  pages = {261--265}
}

@ARTICLE{CHO88a,
  author = {W. Cho and A.G. Tomasselli and R.L. Heinrikson and F.J. K{\'e}zdy},
  title = {The chemical basis for interfacial activation of monomeric phospholipase
	{A$_2$}},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {11237--11241},
  annote = {acylation of Lys-56}
}

@ARTICLE{CHO88,
  author = {Z. H. Cho and C. B. Ahn and S. C. Juh and H. K. Lee and R. E. Jacobs
	and S. Lee and J. H. Yi and J. M. Jo},
  title = {Nuclear magnetic resonance microscopy with 4\,$\mu$m resolution:
	Theoretical study and experimental results},
  journal = {Med.~Phys.},
  year = {1988},
  volume = {15},
  pages = {815--824},
  number = {6},
  annote = {and references therein}
}

@ARTICLE{CLAR88,
  author = {S. A. Clark and others},
  title = {Receptive Fields in the Body-Surface Map in Adult Cortex Defined
	by Temporally Correlated Inputs},
  journal = NAT,
  year = {1988},
  volume = {332},
  pages = {444--445}
}

@BOOK{COHE88,
  title = {Calmodulin},
  publisher = {Elsevier Science Publishers},
  year = {1988},
  author = {P. Cohen and C. B. Klee},
  address = {Amsterdam, The Netherlands}
}

@ARTICLE{COMB88,
  author = {Cecile Combeau and Marie-France Carlier},
  title = {Probing the Mechanism of {ATP} Hydrolysison {F}-actin using Vandate
	and the Structural Analogs of Phosphate ${BeF_{3}^{-}}$ and ${AlF_{4}^{-}}$},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {17429--17436}
}

@ARTICLE{Creu88,
  author = {Michael Creutz},
  title = {Global {M}onte {C}arlo algorithms for many-fermion systems},
  journal = PRD,
  year = {1988},
  volume = {38},
  pages = {1228--1238},
  number = {4}
}

@BOOK{CRIP88,
  title = {Distance Geometry and Molecular Conformation},
  publisher = {Research Studies Press},
  year = {1988},
  author = {Crippen, G. and T. Havel},
  address = {Taunton, Somerset, England}
}

@ARTICLE{CUSA88,
  author = {S. Cusack and J. Smith and J. Finney and B. Tider and M. Karplus},
  title = {Inelastic Neutron Scattering Analysis of Picosecond Internal Protein
	Dynamics},
  journal = JMB,
  year = {1988},
  volume = {202},
  pages = {903--908}
}

@ARTICLE{DANC88,
  author = {Z. Dancshazy and T. G. Ebrey and R. Govindjee},
  title = {Independent Photocycles of the Spectrally Distinct Forms of Bacteriorhodopsin},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {6358--6361}
}

@ARTICLE{DEVR88,
  author = {P. N. Devreotes and S. H. Zigmond},
  title = {Chemotaxis in eukaryotic cells: a focus on leukocytes and {{\em Dictyostelium}}},
  journal = ARCB,
  year = {1988},
  volume = {4},
  pages = {649--686}
}

@ARTICLE{DIFF88,
  author = {J. F. Diffley and B. Stillman},
  title = {A close relative of the nuclear, chromosomal high-mobility group
	protein {HMG1} in yeast mitochondria},
  journal = PNAS,
  year = {1988},
  volume = {88},
  pages = {7864--7868}
}

@ARTICLE{DILL88A,
  author = {K.A. Dill and D. Stigter},
  title = {Lateral interactions among phosphatidylcholine and phosphatidylethanolamine
	head groups in phospholipid monolayers and bilayers},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {3446--3453}
}

@ARTICLE{DILL88,
  author = {R. Diller and M. Stockburger},
  title = {Kinetic Resonance {Raman} Studies Reveal Different Conformational
	States of Bacteriorhodopsin},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {7641--7651}
}

@ARTICLE{DOBL88,
  author = {J. Dobler and W. Zinth and W. Kaiser and D. Oesterhelt},
  title = {Excited-State Reaction Dynamics of Bacteriorhodopsin Studied by Femtosecond
	Spectroscopy},
  journal = CPL,
  year = {1988},
  volume = {144},
  pages = {215--220}
}

@ARTICLE{DONN88,
  author = {Robert A. Donnelly and Rogers, Jr., Jack W.},
  title = {A Discrete Search Technique for Global Optimization},
  journal = IJQCS,
  year = {1988},
  volume = {22},
  pages = {507--513},
  annote = {better (simpler, faster, deeper extrema) then simulated annealing,
	but I think their improvement is marginal and not significant},
  keywords = {model geometry optimization}
}

@ARTICLE{DuNe88,
  author = {D.~H.~E.~Dubin and T.~M.~ O'Neil},
  title = {Computer Simulation of Ion Clouds in a Penning Trap},
  journal = PRL,
  year = {1988},
  volume = {60},
  pages = {511--514},
  number = {6}
}

@ARTICLE{DYSO88a,
  author = {H. J. Dyson and M. Rance and R. A. Houghton and P. E. Wright and
	R. A. Lerner},
  title = {Folding of Immunogenic Peptide Fragments of Proteins in Water Solution
	II. The Nascent Helix},
  journal = {J.\ Mol.\ Biol.},
  year = {1988},
  volume = {201},
  pages = {201--217}
}

@ARTICLE{DYSO88b,
  author = {H. J. Dyson and M. Rance and R. A. Houghton and P. E. Wright and
	R. A. Lerner},
  title = {Folding of Immunogenic Peptide Fragments of Proteins in Water Solution
	I. Sequence Requirements for the Formation of a Reverse Turn},
  journal = {J.\ Mol.\ Biol.},
  year = {1988},
  volume = {201},
  pages = {161--200}
}

@ARTICLE{ECCL88,
  author = {Joseph Eccles and Barry Honig and Klaus Schulten},
  title = {Spectroscopic Determinants in the Reaction Center of\begin{em} {R}hodo\-pseudo\-monas
	viridis\end{em}},
  journal = BJ,
  year = {1988},
  volume = {53},
  pages = {137--144}
}

@ARTICLE{EDHO88,
  author = {Olle Edholm and Fritz J{\"a}hnig},
  title = {The Structure of a Membrane-Spanning Polypeptide Studied by Molecular
	Dynamics},
  journal = BPC,
  year = {1988},
  volume = {30},
  pages = {279--292},
  annote = {points out problems of direct MDS; dt=2fs; SHAKE all bonds; united
	atom model; uses continuum approach for membrane and water},
  keywords = {glycophorin; hydrophobic effect; membrane-spanning helix; thermal
	fluctuation; molecular dynamics; specific heat},
  publisher = {Elsevier}
}

@ARTICLE{EGBE88,
  author = {E. Egberts and H. J. C. Berendsen},
  title = {Molecular Dynamics Simulation of a Smectic Liquid Crystal With Atomic
	Detail},
  journal = JCP,
  year = {1988},
  volume = {89},
  pages = {3718--3732},
  number = {6},
  annote = {smectic = multilamellar aggregate of bilayers; nice overview of literature;
	80ps simulation; distribution functions of atoms and charges; pair
	correlation functions; electron density functions; trans-gauche and
	reorientational relaxation times; comparision to experiment and previous
	simulation; 3166 atoms; 52~ions; 76~decanol molecules; 526~water
	molecues; periodic boundary in 3D; temp. bath 300K; pressure bath
	1atm; dt=2fs; cut-off=7.5A; SPC-water; epsilon=1; special estat with
	2 distance classes; inclusion of long-range Coulomb interactions;
	they give interaction parameters (radii, energy barriers etc.); 40x40x35.6A;
	analysis of transversal waves; good description of order parameters;
	thorough analysis of very many different features},
  keywords = {order parameter; ion-decanol (single chain with ionic head group)-water
	system; water penetration; multi-bilayer system; SHAKE},
  suggestions = {analyze correlation functions; see annote}
}

@ARTICLE{EVANS88,
  author = {R. M. Evans},
  title = {The Steroid and Thyroid Hormone Receptor Superfamily},
  journal = SCI,
  year = {1988},
  volume = {240},
  pages = {889--895},
  annote = {review of the steroid and thyroid hormone family says that there
	is a superfamily of eukaryotic proteins that's conserved between
	species as diverse as fruit flies and humans ref parker's book}
}

@BOOK{Fatu88,
  title = {Numerical Methods for Initial Value Problem in Ordinary Differential
	Equations},
  publisher = {Academic Press, Inc},
  year = {1988},
  author = {S. O. Fatunla}
}

@INPROCEEDINGS{FEHE88,
  author = {G. Feher and T. R. Arno and M. Y. Okamura},
  title = {The effect of an electric field on the charge recombination rate
	of {$D^+Q_A^-\rightarrow DQ_A$} in reaction centers from {\it Rhodobacter
	sphaeroides} {R}-26},
  booktitle = {The Photosynthetic Bacterial Reaction Center: Struc\-ture and Dynamics},
  year = {1988},
  editor = {J. Breton and A. Vermeglio},
  pages = {271--287},
  address = {New York and London},
  publisher = {Plenum Press}
}

@INPROCEEDINGS{Feng88,
  author = {K. Feng},
  title = {Symplectic Geometry and Numerical Methods in Fluid Dynamics},
  booktitle = {Proc. of Inter. Conf. on Numerical Methods in Fluid Dynamics},
  year = {1988},
  editor = {F. G. Zhuang},
  pages = {1--7},
  address = {Beijing, China}
}

@ARTICLE{FERR88,
  author = {T. E. Ferrin and C. C. Huang and L. E. Jarvis and R. Langridge},
  title = {The \mbox{MIDAS} Database System},
  journal = JMG,
  year = {1988},
  volume = {6},
  pages = {2--12}
}

@ARTICLE{FLEM88,
  author = {G. R. Fleming and J. L. Martin and J. Breton},
  title = {Rate of Primary Electron Transfer in Photosynthetic Reaction Centers
	and Their Mechanistic Implications},
  journal = NAT,
  year = {1988},
  volume = {333},
  pages = {190--192}
}

@ARTICLE{FODO88,
  author = {Fodor, S. P. A. and Ames, J. B. and Gebhard, R. and van den Berg,
	E. M. M. and Stoeckenius, W. and Lugtenburg, J. and Mathies, R. A.},
  title = {Chromophore Structure in Bacteriorhodopsin's {N} Intermediate: Implications
	for the Proton-Pumping Mechanism},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {7097--7101},
  annote = {title was CTMOD}
}

@BOOK{FJLO88,
  title = {Solving Problems on Concurrent Processors, Volume I: general techniques
	and regular problems},
  publisher = {Prentice-Hall},
  year = {1988},
  author = {G.C. Fox and M.A. Johnson and G.A. Lyzenga and S.W. Otto and J.K.
	Salmon and D.W. Walker},
  pages = {608 pp},
  address = {Englewood Cliffs, N.~J.}
}

@BOOK{FOX88,
  title = {Solving Problems on Concurrent Processors},
  publisher = {Prentice Hall},
  year = {1988},
  author = {G. C. Fox and M. A. Johnson and G. A. Lyzenga and S. W. Otto and
	J. K. Salmon and D. W. Walker},
  volume = {1},
  address = {Englewood Cliffs, NJ}
}

@ARTICLE{FRAU88,
  author = {H. Frauenfelder and F. Parak and R.D. Young},
  title = {Conformational Substates in Proteins.},
  journal = ARBBC,
  year = {1988},
  volume = {17},
  pages = {451--79}
}

@ARTICLE{FREE88,
  author = {L.~P.~Freedman and B.~F.~Luisi and Z. R.~Korszun and R.~Basavappa
	and P.~B.~Sigler and K.~R.~Yamamoto},
  title = {The function and structure of the metal coordination sites within
	the glucocorticoid receptor {DNA} binding domain},
  journal = NAT,
  year = {1988},
  volume = {334},
  pages = {543--546},
  annote = {says that the DBD will bind by itself to the specific sequence, neither
	complete or DBD will dimerize w/out DNA.. check this--NO! see hard90
	following is correct. minimium DBD is 70-80 aa with 2zinc binding
	motifs,zinc tetrahedrally ligated by four conserved cysteine ligands
	ref also sevr88}
}

@ARTICLE{GeFe88,
  author = {Z. Ge and K. Feng},
  title = {On the Approximation of Linear \mbox{Hamiltonian} Systems},
  journal = {J. Comput. Math.},
  year = {1988},
  volume = {6},
  pages = {88--97},
  number = {1}
}

@ARTICLE{GeMa88,
  author = {Z. Ge and J. E. Marsden},
  title = {\mbox{Lie--Poisson Hamilton--Jacobi} Theory and \mbox{Lie--Poisson}
	Integrators},
  journal = {Phys. Lett. A},
  year = {1988},
  volume = {133},
  pages = {134--139},
  number = {3}
}

@ARTICLE{GILL88,
  author = {T. Gillbro and R. J. Cogdell and V. Sundstr{\"o}m},
  title = {Energy transfer from carotenoid to bacteriochlorophyll a in the B800-820
	antenna complexes from {\em Rhodopseudomonas acidophila} strain 7050},
  journal = FEBS,
  year = {1988},
  volume = {235},
  pages = {169--172}
}

@ARTICLE{GILS88C,
  author = {H. Gilson and B. Honig},
  title = {Analysis of {NMR} and Absorption Spectroscopic Data in Bacteriorhodopsin:
	Models for Protein-Chromophore Interactions},
  journal = JACS,
  year = {1988},
  volume = {110},
  pages = {1943--1350}
}

@ARTICLE{GILS88A,
  author = {Michael K.\ Gilson and Barry H.\ Honig},
  title = {Energetics of Charge-Charge Interactions in Proteins},
  journal = {Proteins},
  year = {1988},
  volume = {3},
  pages = {32--52}
}

@ARTICLE{GILS88B,
  author = {Michael K.\ Gilson and Barry H.\ Honig},
  title = {Calculation of the Total Electrostatic Energy of a Macromolecular
	System: Solvation Energies, Binding Energies, and Conformational
	Analysis},
  journal = {Proteins},
  year = {1988},
  volume = {4},
  pages = {7--18}
}

@ARTICLE{GRSP88,
  author = {MM. Gottardis and SP. Robinson and PG. Satyaswaroop and VC. Jordan},
  title = {Contrasting actions of tamoxifen on endometrial and breast tumor
	growth in the athymic mouse},
  journal = {Cancer Research},
  year = {1988},
  volume = {48},
  pages = {812--815}
}

@BOOK{Gree88c,
  title = {The Rapid Evaluation of Potential Fields in Particle Systems},
  publisher = {MIT Press},
  year = {1988},
  author = {Leslie Greengard},
  address = {Cambridge}
}

@TECHREPORT{GREE88A,
  author = {L. Greengard and W. D. Gropp},
  title = {A parallel version of the fast multipole method},
  institution = {Rept. YALEU/DCS/RR-640},
  year = {1988}
}

@TECHREPORT{GrGr88,
  author = {L. Greengard and W. D. Gropp},
  title = {A Parallel Version of the Fast Multipole Method},
  institution = {Yale Univ.},
  year = {1988},
  number = {YALEU/DCS/RR-640}
}

@TECHREPORT{GREE88B,
  author = {L. Greengard and V. Rokhlin},
  title = {On the efficient implementation of the fast multipole algorithm},
  institution = {Rept. YALEU/DCS/RR-602},
  year = {1988}
}

@TECHREPORT{GrRo88,
  author = {L. Greengard and V. Rokhlin},
  title = {On the efficient implementation of the fast multipole algorithm},
  institution = {Yale Univ.},
  year = {1988},
  number = {YALEU/DCS/RR-602}
}

@ARTICLE{Gree88,
  author = {D. Greenspan},
  title = {An Explicit Energy-Conserving Numerical Method for Equations of the
	Form $\frac{d^2 x}{dt^2}= f(x)$},
  journal = {J. Comput. Phys.},
  year = {1988},
  volume = {79},
  pages = {473--476}
}

@ARTICLE{GrSH88,
  author = {A. Greiner and W. Strittmatter and J. Honerkamp},
  title = {Numerical Integration of Stochastic Differential Equations},
  journal = {J. Statist.\ Phys.},
  year = {1988},
  volume = {51},
  pages = {95--108}
}

@ARTICLE{GRIS88A,
  author = {C. B. Grissom and W. W. Cleland},
  title = {Isotope Effect Studies of Chicken Liver NADP Malic Enzyme: Role of
	the Metal Ion and Viscosity Dependence},
  journal = {Biochemistry},
  year = {1988},
  volume = {27},
  pages = {2927--2934}
}

@ARTICLE{GRIS88B,
  author = {C. B. Grissom and W. W. Cleland},
  title = {Isotope Effect Studies of the Chemical Mechanism of Pig Heart NADP
	Isocitrate Dehydrogenase},
  journal = {Biochemistry},
  year = {1988},
  volume = {27},
  pages = {2934--2943}
}

@INPROCEEDINGS{VANG88,
  author = {R. van Grondelle and V. Sundstrom},
  title = {Excitation energy transfer in photosynthesis},
  booktitle = {Photosynthetic Light--Harvesting Systems},
  year = {1988},
  editor = {H. Scheer},
  pages = {403--438},
  address = {Berlin, New York},
  publisher = {Walter de Gruyter \& Co.}
}

@ARTICLE{GRUB88,
  author = {Helmut Grubm{\"u}ller and Helmut Heller and Klaus Schulten},
  title = {Eine {Cray} f\"ur 100.000~{DM}},
  journal = MCM,
  year = {1988},
  volume = {11},
  pages = {48--64}
}

@ARTICLE{GRUN88,
  author = {S. M. Gruner and M. W. Tate and G. L. Kirk and P. T. C. So and D.
	C. Turner and D. T. Keane and P. S. Tilcock and P. R. Cullis},
  title = {X-ray diffraction study of polymorphic behaviour of {N}-methylated
	dioleoylphosphatidylethanolamine},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {2853--2866},
  annote = {requested Tx=19920908., surface area per head group in excess water
	for DOPC is 70\AA^2}
}

@ARTICLE{HACK88,
  author = {D.D. Hackney},
  title = {Kinesin {ATP}ase: Rate-limiting {ADP} release},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {6314--6318}
}

@ARTICLE{HAGE88,
  author = {Paul J. Hagerman},
  title = {Flexibility of {DNA}},
  journal = ARBBC,
  year = {1988},
  volume = {17},
  pages = {265--286}
}

@ARTICLE{HEID88,
  author = {D.B. Heidorn and J. Trewhella},
  title = {Comparison of the crystal and solution structures of calmodulin and
	troponin {C}},
  journal = {Biochemistry},
  year = {1988},
  volume = {27},
  pages = {909--15}
}

@MASTERSTHESIS{HELL88,
  author = {Helmut Heller},
  title = {{D}ynamiksimulation sehr gro\ss er {M}akromolek\"ule am {B}eispiel
	des photosynthetischen {R}eaktionszentrums von {R}hodopseudomonas
	viridis},
  school = {{T}echnical {U}niversity of {M}unich, {P}hysics Department, T~30},
  year = {1988},
  type = {Diploma Thesis},
  address = {James-Franck-Street, D-8046~Garching / Munich}
}

@ARTICLE{HERZ88,
  author = {O. Herzberg and M.N.G. James},
  title = {Refined Crystal Structure of TRoponin C from Turkey skeletal Muscle
	at 2.0 {{\AA}} Resolution},
  journal = {J. Mol. Biol.},
  year = {1988},
  volume = {203},
  pages = {761--779}
}

@ARTICLE{HEYN88,
  author = {M. P. Heyn and J. Westerhausen and I. Wallat and F. Seiff},
  title = {High-Sensitivity Neutron-Diffraction of Membranes\ --\ Location of
	the {Schiff}-Base End of the Chromophore of Bacteriorhodopsin},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {2146--2150}
}

@ARTICLE{HYDE88,
  author = {C. Craig Hyde and S. Ashrafudin Ahmed and Eduardo A. Padlan and Edith
	W. Miles and David R. Davies},
  title = {Three-dimensional structure of the tryptophan synthase $\alpha_2
	\beta_2$ multienzyme complex from {{\it Salmonella typhimurium}}},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {17857--17871}
}

@ARTICLE{ICHI88,
  author = {T.~Ichiye and M.~Karplus},
  title = {Anisotropy and anharmonicity of atomic fluctuations in proteins:
	implications for X-Ray analysis.},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {3487--3497}
}

@ARTICLE{JoFo88,
  author = {R.~E. Johnson and B. Foote},
  title = {Designing reusable classes},
  journal = JOOP,
  year = {1988}
}

@ARTICLE{JORD88,
  author = {S. R. Jordan and C. O. Pabo},
  title = {Structure of the Lambda Complex at 2.5\,{\AA\ } Resolution: Details
	of the Repressor-Operator Interactions},
  journal = SCI,
  year = {1988},
  volume = {242},
  pages = {893--899}
}

@ARTICLE{JoTi88,
  author = {W.J.~Jorgensen and J.~Tirado-Rives},
  title = {The {OPLS} Potential Functions for Protein Energy Minimization for
	Crystals of Cyclic Peptides and Crambin},
  journal = JACS,
  year = {1988},
  volume = {110},
  pages = {3469}
}

@BOOK{KeRi88,
  title = {The C Programming Language - Second Edition},
  publisher = {Prentice-Hall},
  year = {1988},
  author = {B. W. Kernighan and D. M. Ritchie}
}

@ARTICLE{KHOR88,
  author = {H. G. Khorana},
  title = {Bacteriorhodopsin, a Membrane Protein That Uses Light to Translocate
	Protons},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {7439--7442}
}

@INPROCEEDINGS{KIRM88,
  author = {C. Kirmaier and D. Holten},
  title = {Temperature Effects on the Ground State Absorption Spectra and Electron
	Transfer Kinetics of Bacterial Reaction Centers},
  booktitle = {The Photosynthetic Bacterial Reaction Center: Struc\-ture and Dynamics},
  year = {1988},
  editor = {J. Breton and A. Vermeglio},
  pages = {219--228},
  address = {New York and London},
  publisher = {Plenum Press}
}

@ARTICLE{KOUY88,
  author = {T. Kouyama and A. M. Kouyama and A. Ikegami and M. K. Mathew and
	W. Stoeckenius},
  title = {Bacteriorhodopsin Photoreaction\ --\ Identification of a Long-Lived
	Intermediate {N} ({P}, {R}350) at High {pH} and Its {M}-Like Photoproduct},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {5855--5863}
}

@ARTICLE{KUHA88,
  author = {R. A. Kuharsky and J. S. Bader and D. Chandler and M. Sprik and M.
	L. Klein and R. W. Impey},
  title = {Molecular Model for Aqueous Ferrous--Ferric Electron Transfer},
  journal = JCP,
  year = {1988},
  volume = {89},
  pages = {3248--3257}
}

@ARTICLE{KUMA88,
  author = {V.~Kumar and P.~Chambon},
  title = {The oestrogen receptor binds tightly to its responsive element as
	a ligand induced homodimer.},
  journal = {Cell},
  year = {1988},
  volume = {55},
  pages = {145--156},
  annote = {proves that ER binds as a homodimer}
}

@ARTICLE{KuWa88,
  author = {S. Kuwajima and A. Warshel},
  title = {The extended {E}wald method -- {A} general treatment of long-range
	lectrostatic interactions in microscopic simulations},
  journal = {J. Chem. Phys.},
  year = {1988},
  volume = {89},
  pages = {3751--3759}
}

@ARTICLE{GORD88,
  author = {L.M.Gordon and F.C.Jensen and C.C.Curtain and P.W.Mobley and R.C.Aloia},
  title = {Thermotropic Lipid Phase Separation in the Human Immunodeficiency
	Virus},
  journal = BBA,
  year = {1988},
  volume = {943},
  pages = {331--342}
}

@ARTICLE{Lasa88,
  author = {F. M. Lasagni},
  title = {Canonical \mbox{Runge-Kutta} methods},
  journal = {J. Appl. Math. Phys.(ZAMP)},
  year = {1988},
  volume = {39},
  pages = {952--953}
}

@ARTICLE{LAVE88,
  author = {R.~Lavery and H.~Sklenar},
  title = {The definition of generalized helicoidal parameters and of axis curvature
	for irregular nucleic acids.},
  journal = {J.\ Biomol.\ Str.\ Dyn.},
  year = {1988},
  volume = {6},
  pages = {63--91},
  annote = {use as reference to MDtoolchest if analyzed DNA, add above also}
}

@ARTICLE{LEAR88,
  author = {James D. Lear and Z. R. Wasserman and W. F. DeGrado},
  title = {Synthetic Amphiphilic Peptide Models for Protein Ion Channels},
  journal = SCI,
  year = {1988},
  volume = {240},
  pages = {1177--1181}
}

@ARTICLE{LEVI88,
  author = {Michael Levitt and Ruth Sharon},
  title = {Accurate Simulation of Protein Dynamics in Solution},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {7557--7561}
}

@ARTICLE{LiQi88,
  author = {C.-W. Li and M.-Z. Qin},
  title = {A Symplectic Difference Scheme for the Infinite Dimensional \mbox{Hamilton}
	Systems},
  journal = {J. Comput. Math.},
  year = {1988},
  volume = {6},
  pages = {164--174},
  number = {2}
}

@ARTICLE{LIVI91,
  author = {J.~R.~Livingstone and R.~S.~Spolar and M.~T.~Record},
  title = {Contribution of the thermodynamics of protein folding from the reduction
	in water-accessible non-polar surface area.},
  journal = BCH,
  year = {1988},
  volume = {30},
  pages = {4237--4244}
}

@ARTICLE{LoMe88,
  author = {P. Lochak and C. Meunier},
  title = {Multiphase Averaging For Classical Systems: With Applications to
	Adiabatic Theorems},
  year = {1988},
  address = {New York},
  nremark = {515.35L787M, reviewed in SIREV 1991, p. 495},
  publisher = {Springer-Verlag}
}

@INPROCEEDINGS{MART88,
  author = {J. L. Martin and J. Breton and J. C. Lambry and G. Fleming},
  title = {The Primary Electron Transfer in Photosynthetic Purple Bacteria:
	Long Range Electron Transfer in the Femtosecond Domain at Low Temperature},
  booktitle = {The Photosynthetic Bacterial Reaction Center: Struc\-ture and Dynamics},
  year = {1988},
  editor = {J. Breton and A. Vermeglio},
  pages = {195--203},
  address = {New York and London},
  publisher = {Plenum Press}
}

@ARTICLE{MATH88,
  author = {R. A. Mathies and C. H. {Brito Cruz} and W. T. Pollard and C. V.
	Shank},
  title = {Direct Observation of the Femtosecond Excited-State {\it cis-trans}
	Isomerization in Bacteriorhodopsin},
  journal = SCI,
  year = {1988},
  volume = {240},
  pages = {777--779}
}

@ARTICLE{MIES88,
  author = {R.~Meisfeld and D.~Sennis and A.~Inoue and M.~Schena and P.~J.~Godowski
	and K.~R.~Yamamoto},
  title = {Glucocorticoid Receptor Sequences That Confer Positive and Negative
	Transcriptional Regulation},
  journal = {Steroid Hormone Action},
  year = {1988},
  pages = {193--200},
  annote = {isolates the DBD}
}

@ARTICLE{MILD88,
  author = {S. J. Milder and D. S. Kliger},
  title = {A Time-Resolved Spectral Study of the {K} and {KL} Intermediates
	of Bacteriorhodopsin},
  journal = BJ,
  year = {1988},
  volume = {53},
  pages = {465--468}
}

@ARTICLE{MOGI88,
  author = {Mogi,T. and Stern,L.J. and Marti,T. and Chao, B.H. and Khorana,H.G.},
  title = {Aspartic acid substitutions affect proton translocation by bacteriorhodopsin},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {4148--4152}
}

@ARTICLE{MOSK88,
  author = {C. Moskaluk and D. Bastia},
  title = {{DNA} bending is induced in an enhancer by the {DNA}-binding domain
	of the bovine papillomavirus {sc E2}.},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {1826--1830},
  annote = {not read, eukaryotic bending DNA}
}

@ARTICLE{MULL88,
  author = {N. Muller},
  title = {Is There a Region of Highly Structured Water Around a Nonpolar Solute
	Molecule?},
  journal = JSC,
  year = {1988},
  volume = {17},
  pages = {661--672}
}

@ARTICLE{NADL88,
  author = {Walter Nadler and Klaus Schulten},
  title = {Mean Relaxation Time Approximation for Dynamical Correlation Functions
	in Stochastic Systems near Instabilities: {II}.\ {T}he Single Mode
	Laser},
  journal = ZP,
  year = {1988},
  volume = {72},
  pages = {535--543}
}

@ARTICLE{NAGL88,
  author = {J. F. Nagle and M. C. Wiener},
  title = {Structure of fully hydrated bilayer dispersions},
  journal = BBA,
  year = {1988},
  volume = {942},
  pages = {1--10},
  annote = {C-phase=crystal phase=L_c; G-phase=gel phase=L_\beta'; F-phase=fluid
	phase=L_\alpha; rigorous definitions for many quantities like volumes
	and areas of lipids, etc; contains a table with many experimental
	values; compares different incongruent experimental results from
	other groups; confusing; fluid phase of DPPC is experimentally not
	well defined but very well studied},
  keywords = {lipid; multilamellar dispersion; bilayer structure; membrane; molecular
	volume; area per lipid; DPPC; DLPE; tilt; hydration states; experimental}
}

@ARTICLE{NILG88,
  author = {M. Nilges and G. M. Clore and A. M. Gronenborn},
  title = {Determination of three-dimensional structures of proteins from interproton
	distance data by simulated annealing from a random array of atoms},
  journal = FEBS,
  year = {1988},
  volume = {239},
  pages = {129--136}
}

@BOOK{LOVE88,
  title = {Progress in Clinical and Biological Research Vol.257: Electromagnetic
	Fields and Neurobehavioral Function},
  publisher = {Alan R. Liss, Inc.},
  year = {1988},
  author = {Mary Ellen O'Connor and Richard H. Lovely},
  address = {New York}
}

@ARTICLE{OAS88,
  author = {T. G. Oas and P. S. Kim},
  title = {A Peptide Model of a Protein Folding Intermediate},
  journal = NAT,
  year = {1988},
  volume = {336},
  pages = {42--48}
}

@ARTICLE{VAN+88,
  author = {E. Van Obberghen-Schilling and N.S. Roche and K.C. Flanders and M.B.
	Sporn and A. Roberts},
  title = {Transforming growth factor {B}eta-1 positively regulates its own
	expression in normal and transformed cells},
  journal = {J. Biol. Chem.},
  year = {1988},
  volume = {263},
  pages = {7741--7746}
}

@ARTICLE{OTWI88,
  author = {Z.~Otwinowski and R.~W.~Schevitz and R.~G.~Zhang and C.~L.~Lawson
	and A.~Joachimiak and R.~Q.~Marmorstein and B.~F.~Luisi and P.~B.~Sigler.},
  title = {Crystal structure of the {\em trp} repressor/operator complex at
	atomic resolution},
  journal = NAT,
  year = {1988},
  volume = {335},
  pages = {321--329}
}

@ARTICLE{PaBS88,
  author = {R. W. Pastor and B. R. Brooks and A. Szabo},
  title = {An Analysis of the Accuracy of {L}angevin and Molecular Dynamics
	Algorithm},
  journal = {Mol. Phys.},
  year = {1988},
  volume = {65},
  pages = {1409--1419}
}

@ARTICLE{PAST88,
  author = {Richard W. Pastor and Richard M. Venable and Martin Karplus},
  title = {Brownian Dynamics Simulation of a Lipid Chain in a Membrane Bilayer},
  journal = JCP,
  year = {1988},
  volume = {89},
  pages = {1112--1127},
  annote = {only one chain of one molecule is simulated; simulation time: 0.66\,\mu
	s; order parameter without explicite hydrogens; some experimental
	data; dt=1.5fs; friction coefficient=150/ps; gives isomerization
	rates},
  keywords = {diplamitoyl phosphatidylcholine DPPC; membrane; brownian dynamics;
	dihedral angles; Marcelja mean field; order parameter},
  suggestions = {tilt!}
}

@ARTICLE{PAST88A,
  author = {Richard W. Pastor and Richard M. Venable and Martin Karplus and Attila
	Szabo},
  title = {A Simulation Based Model of {NMR $T_1$} Relaxation in Lipid Bilayer
	Vesicles},
  journal = JCP,
  year = {1988},
  volume = {89},
  pages = {1128--1140},
  number = {2},
  annote = {DPPC vesicles; time correlation functions from trajectory; $\gamma$
	ranges from 47~ps$^{-1}$ to 150~ps$^{-1}$; best fit with around 50~ps$^{-1}$;
	analysis of trajectory data},
  keywords = {wobbling in a cone; nematic liquid crystal; correlation functions;
	order parameter; viscosity; rotational diffusion},
  suggestions = {look at tilt and its origin: single molecule or collective}
}

@ARTICLE{PERL88,
  author = {T.~Perlmann and {\"O}.~Wrange},
  title = {Specific glucocorticoid receptor binding to {DNA} reconstituted in
	a nucleosome},
  journal = EMBO,
  year = {1988},
  volume = {7},
  pages = {3073--3079},
  number = {10},
  annote = {GRE in MMTV located nuclesome and is altered by GR binding says that
	GR DID in fact induce local alterations in DNA}
}

@ARTICLE{PePe88,
  author = {John W. Perram and Henrik G. Petersen},
  title = {algorithms for computing the dynamical trajectories of flexible bodies},
  journal = {molecular physics},
  year = {1988},
  volume = {65},
  pages = {861--874},
  number = {4}
}

@ARTICLE{PePL88,
  author = {J. W. Perram and H. G. Petersen and S. W. de Leeuw},
  title = {An algorithm for the simulation of condensed matter which grows as
	the $\frac{3}{2}$ power of the number of particles},
  journal = {Mol. Phys.},
  year = {1988},
  volume = {65},
  pages = {875--893}
}

@ARTICLE{POIR88,
  author = {R.~A.~Poirier and A.~Yadav and P.~R.~Surjan},
  title = {{A Preliminary Ab Initio Investigation of Retinal Analogs}},
  journal = {J. Mol. Struct. (Theochem)},
  year = {1988},
  volume = {167},
  pages = {321--329}
}

@ARTICLE{PRUZ88,
  author = {W. Pruzanski and P. Vadas},
  title = {Secretory synovial fluid phospholipase {A}$_2$ and its role in the
	pathogenesis of inflammation in arthritis},
  journal = {J. Rheumatol.},
  year = {1988},
  volume = {15},
  pages = {1601--1603},
  annote = {Pharmaceutical aspecst of PLA2, get it.}
}

@ARTICLE{QIAN88,
  author = {N. Qian and T. J. Sejnowski},
  title = {Predicting the Secondary Structure of Globular Proteins Using Neural
	Network Models},
  journal = JMB,
  year = {1988},
  volume = {202},
  pages = {865--884}
}

@ARTICLE{Qin88,
  author = {C.-Y. Qin},
  title = {An explicit Energy-Conserving Numerical Method for Equations of the
	form $\ddot{x} = f(x)$},
  journal = {J. Comput. Phys.},
  year = {1988},
  volume = {79},
  pages = {473--476}
}

@ARTICLE{ALOI88,
  author = {R.C.Aloia and F.C.Jensen and C.C.Curtain and P.W.Mobley and L.M.Gordon},
  title = {Lipid Composition and Fluidity of the Human Immunodeficiency Virus},
  journal = PNAS,
  year = {1988},
  volume = {85},
  pages = {900--904}
}

@ARTICLE{RADZ88,
  author = {Anna Radzicka and Richard Wolfenden},
  title = {Comparing the Polarities of the Amino Acids: Side Chain Distribution
	Coefficients between the Vapor Phase, Cyclohexane, 1-Octanol, and
	Neutral Aqueous Solution},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {1664--1670}
}

@ARTICLE{RAND88,
  author = {R.P. Rand and N. Fuller and V.A. Parsegian and D.C. Rau},
  title = {Variation in hydration forces between neutral phospholipid bilayers:
	evidence for hydration attraction},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {7711}
}

@ARTICLE{Rapa88,
  author = {D.~C. Rapaport},
  title = {Large-Scale Molecular Dynamics Simulation Using Vector and Parallel
	Computers},
  journal = {Computer Physics Reports},
  year = {1988},
  volume = {9},
  pages = {1--53}
}

@ARTICLE{RICH91,
  author = {F. M. Richards},
  title = {The Protein Folding Problem},
  journal = SA,
  year = {1988},
  pages = {54--63}
}

@INCOLLECTION{RITT88,
  author = {Helge Ritter and Klaus Schulten},
  title = {Extending {K}ohonen's Self-Organizing Mapping Algorithm to Learn
	Ballistic Movements},
  booktitle = {Neural Computers},
  publisher = {Springer--Verlag},
  year = {1988},
  editor = {R. Eckmiller and Ch. von der Malsburg},
  volume = {41},
  series = {NATOF},
  pages = {393--406}
}

@INPROCEEDINGS{RITT88A,
  author = {Helge Ritter and Klaus Schulten},
  title = {{K}ohonen's Self-Organizing Maps: Exploring their Computational Capabilities},
  booktitle = {IEEE International Conference on Neural Networks, San Diego, California,
	July 24--27, 1988},
  year = {1988},
  volume = {1},
  pages = {109--116},
  address = {New York},
  publisher = {The Institute of Electrical and Electronics Engineers}
}

@ARTICLE{RITT88B,
  author = {Helge Ritter and Klaus Schulten},
  title = {Convergence Properties of {K}ohonen's Topology Conserving Maps: Fluctuations,
	Stability and Dimension Selection},
  journal = BC,
  year = {1988},
  volume = {60},
  pages = {59--71},
  number = {1}
}

@ARTICLE{RODE88,
  author = {H. Roder and G. A. Elove and S. W. Englander},
  title = {Structural Characterization of Folding Intermediates in Cytochrome~c
	by {H}-Exchange Labelling and Proton {NMR}},
  journal = NAT,
  year = {1988},
  volume = {335},
  pages = {700--704}
}

@ARTICLE{ROEP88,
  author = {P. D. Roepe and P. L. Ahl and J. Herzfeld and J. Lugtenburg and K.
	J. Rothschild},
  title = {Tyrosine Protonation Changes in Bacteriorhodopsin},
  journal = JBC,
  year = {1988},
  volume = {263},
  pages = {5110--5117}
}

@ARTICLE{ROMM88,
  author = {E. Rommel and F. Noack and P. Meier and G. Kothe},
  title = {Proton spin relaxation dispersion studies of phospholipid membranes},
  journal = JPC,
  year = {1988},
  volume = {92},
  pages = {2981--2987}
}

@ARTICLE{SANY88,
  author = {G. Sanyal and L.M. Richard and K.L. Carraway and D. Puett},
  title = {Binding of Amphiphilic Peptides to Carboxy-Terminal Tryptic Fragment
	of Calmodulin},
  journal = BCH,
  year = {1988},
  volume = {27},
  pages = {6229--6236}
}

@ARTICLE{Sanz88,
  author = {J. M. Sanz-Serna},
  title = {\mbox{Runge-Kutta} Schemes for \mbox{Hamiltonian} Systems},
  journal = {BIT},
  year = {1988},
  volume = {28},
  pages = {877--883}
}

@ARTICLE{SATY88,
  author = {K.A. Satyshur and S.T. Rao and D. Pyzalska and W. Drendel and M.
	Greaser and M. Sundaralingam},
  title = {Refined Structure of Chicken skeletal Muscle Troponin {C} in the
	Two-calcium State at 2-{{\AA}} Resolution},
  journal = {J. Biol. Chem.},
  year = {1988},
  volume = {263},
  pages = {1628--1647}
}

@ARTICLE{SEJN88,
  author = {T. Sejnowski and C. Koch and P. Churchland},
  title = {Computational Neuroscience},
  journal = SCI,
  year = {1988},
  volume = {241},
  pages = {1299--1306}
}

@ARTICLE{SESS88,
  author = {R. Sessions and P. Dauber-Osguthorpe and D. Osguthorpe},
  title = {Filtering Molecular Dynamics Trajectories to Reveal Low-frequancy
	Collective Motions: Phospholipase A2},
  journal = JMB,
  year = {1988},
  volume = {209},
  pages = {617--633}
}

@ARTICLE{SEVE88,
  author = {Y.~Severne and S.~Wieland and W.~Schaffner and S.~Rusconi},
  title = {Metal binding ``finger'' structures in the glucocorticoid receptor
	defined by site--directed mutagenesis},
  journal = EMBO,
  year = {1988},
  volume = {7},
  pages = {2503--2508},
  annote = {along with free88 says that minimium DBD is 70-80 aa with 2zinc binding
	motifs,zinc tetrahedrally ligated by four conserved cysteine ligands}
}

@ARTICLE{SIRO88,
  author = {E. B. Sirota and C. R. Safinya and R. J. Plano and N. A. Clark},
  title = {X-ray scattering studies of aligned, stacked surfactant membranes},
  journal = SCI,
  year = {1988},
  volume = {242},
  pages = {1406--1409},
  annote = {requested Tx=19920908.}
}

@ARTICLE{SPER88,
  author = {M.M. Sperotto and O.G. Mouritsen},
  title = {Dependence of lipid membrane phase transition temperature on the
	mismatch of protein and lipid hydrophobic thickness},
  journal = {Eur. Biophys. J},
  year = {1988},
  volume = {16},
  pages = {1--10}
}

@ARTICLE{STEH88,
  author = {J. Stehle and S. Reuss and H. Schroder and M. Henschel and L. Vollrath},
  title = {Magnetic Field Effects on Pineal N-Acetyltransferase Activity and
	Melatonin Content in the Gerbil-Role of Pigmentation and Sex},
  journal = {Physiology and Behavior},
  year = {1988},
  volume = {44},
  pages = {91--94}
}

@PHDTHESIS{Stof88,
  author = {Daniel M. Stoffer},
  title = {Some Geometric and Numerical Methods for Perturbed Integrable Systems},
  school = {Swiss Federal Institute of Technology},
  year = {1988},
  address = {Z\"urich}
}

@BOOK{STRY88,
  title = {Biochemistry},
  publisher = {W. H. Freeman and Company},
  year = {1988},
  author = {L. Stryer},
  address = {New York},
  edition = {3rd}
}

@INPROCEEDINGS{Suri88,
  author = {Y.B. Suris},
  title = {Preservation of symplectic structure in the numerical solution of
	{H}amiltonian systems},
  booktitle = {Numerical Solution of Differential Equations},
  year = {1988},
  pages = {148--160 (in Russian)},
  address = {Akad. Nauk. SSSR, Inst. Prikl. Mat., Moscow},
  edit = {S.S. Filippov},
  nremark = {Chislennoye Resheniye Obyknovennykh Differentsialnykh Uravnenii (Numerical
	Solution of Ordinary Differential Equations), Filippov, S.S., Ed.,
	Moscow: Keldysh Inst. Appl. Math., USSR Acad. Sci., 1988, pp. 148
	- 160 (in Russian)}
}

@INCOLLECTION{TAVA88,
  author = {Paul Tavan and Klaus Schulten},
  title = {Quasiparticle Excitations in Polyenes and Polyacetylene},
  booktitle = {Nonlinear Optical Properties of Polymers},
  publisher = {Materials Research Society},
  year = {1988},
  editor = {A. J. Heeger and J. Orenstein and D. Ulrich},
  volume = {109},
  series = {Symposium Proceedings},
  pages = {163--170},
  address = {Pittsburgh}
}

@ARTICLE{THAN88,
  author = {N. Thanki and J. M. Thornton and J. M. Goodfellow},
  title = {Distributions of Water Around Amino Acid Residues in Proteins},
  journal = JMB,
  year = {1988},
  volume = {202},
  pages = {637--657}
}

@ARTICLE{THOM88,
  author = {J.~F.~Thompson and A.~Landy},
  title = {Empirical estimate of protein-induced {\sc DNA} bending angles: applications
	to lambda site-specific recombinaton complexes.},
  journal = {Nucleic Acids Research},
  year = {1988},
  volume = {16},
  pages = {9687--9705},
  annote = {equation for determining degree of bending from mobility i think
	it was the original paper on this method}
}

@ARTICLE{ToBr88,
  author = {D.~J. Tobias and C. L. Brooks},
  title = {Molecular Dynamics with Internal Coordinate Constraints},
  journal = {J. Chem Phys.},
  year = {1988},
  volume = {89},
  pages = {5115--5127}
}

@PHDTHESIS{TREU88,
  author = {Herbert Treutlein},
  title = {{M}olekulardynamiksimulation des {R}eaktionszentrums von {R}hodopseudomonas
	viridis},
  school = {{T}echnische {U}niversit\"at {M}\"unchen, {P}hysik-Department, T~30},
  year = {1988},
  type = {Doktorarbeit},
  address = {James-Franck-Stra{\ss}e, 8046~Garching}
}

@INCOLLECTION{TREU88D,
  author = {Herbert Treutlein and Christoph Niedermeier and Klaus Schulten and
	J. Deisenhofer and H. Michel and Axel Br{\"u}nger and Martin Karplus},
  title = {Molecular Dynamics Simulation of the Primary Processes in the \mbox{Photosynthetic}
	Reaction Center of\begin{em} {R}hodopseudomonas viridis\end{em}},
  booktitle = {Transport Through Membranes: Carriers, Channels and Pumps},
  publisher = {Kluwer Academic Publishers},
  year = {1988},
  editor = {A. Pullman and others},
  pages = {513--525},
  address = {Dordrecht}
}

@INCOLLECTION{TREU88B,
  author = {Herbert Treutlein and Klaus Schulten and J. Deisenhofer and H. Michel
	and Axel Br{\"u}nger and Martin Karplus},
  title = {Molecular Dynamics Simulation of the Primary Processes in the Photosynthetic
	Reaction Center of\begin{em} {R}hodopseudomonas viridis\end{em}},
  booktitle = {The Photosynthetic Bacterial Reaction Center: Structure and Dynamics},
  publisher = {Plenum},
  year = {1988},
  editor = {J. Breton and A. Verm{\'e}glio},
  volume = {149},
  series = NATOA,
  pages = {139--150},
  address = {New York}
}

@INCOLLECTION{TREU88C,
  author = {Herbert Treutlein and Klaus Schulten and Christoph Niedermeier and
	J. Deisenhofer and H. Michel and D. Devault},
  title = {Electrostatic Control of Electron Transfer in the Photosynthetic
	Reaction Center of\begin{em} {R}hodo\-pseudomonas viridis\end{em}},
  booktitle = {The Photosynthetic Bacterial Reaction Center: Structure and Dynamics},
  publisher = {Plenum},
  year = {1988},
  editor = {J. Breton and A. Verm{\'e}glio},
  volume = {149},
  series = NATOA,
  pages = {369--377},
  address = {New York}
}

@ARTICLE{TREU88A,
  author = {Herbert Treutlein and Andreas Windemuth and Klaus Schulten},
  title = {{``Molecular Design'' --- Simulation und Graphik von Biomolek\"ulen}},
  journal = MCM,
  year = {1988},
  volume = {1},
  pages = {46--57}
}

@ARTICLE{TURS88,
  author = {P. Turski and T. Kalinke and L. Strother and W. Perman and G. Scott
	and S. Kornguth},
  title = {{MRI of Rabbit Brain after Intracarotic Injection of Large Multivesicular
	Liposomes Containing Paramagnetic Metals and DTPA}},
  journal = MRM,
  year = {1988},
  volume = {{\bf 7}},
  pages = {184--196},
  brief = {(3rd in Magin refs.) (not read)},
  keywords = {liposomes, paramagnetic, Gd-DTPA}
}

@ARTICLE{UDGA88,
  author = {J. B. Udgaonkar and R. L. Baldwin},
  title = {{NMR} Evidence for an Early Framework Intermediate on the Folding
	Pathway of Ribonuclease~{A}},
  journal = NAT,
  year = {1988},
  volume = {335},
  pages = {694--699}
}

@ARTICLE{VADA88a,
  author = { P. Vadas and W. Pruzanski },
  title = {Extracellular phospholipase {A$_2$}: causative agent in circulatory
	collapse of septic shock?},
  journal = {Agents Actions},
  year = {1988},
  volume = {24},
  pages = {320--326},
  annote = {Pharmaceutical aspecst of PLA2, get it.}
}

@ARTICLE{VARO88,
  author = {G. Varo and K. Bryl},
  title = {Light- and Dark-adaptation of Bacteriorhodopsin Measured by a Photoelectric
	Method},
  journal = BBA,
  year = {1988},
  volume = {934},
  pages = {247--252}
}

@ARTICLE{WATA88,
  author = {Kyoko Watanabe and Mauro Ferrario and Miacheal L. Klein},
  title = {Molecular Dynamics Study of a Sodium Octanoate Micelle in Aqueous
	Solution},
  journal = JPC,
  year = {1988},
  volume = {92},
  pages = {819--821},
  annote = {simulation time: 250ps; dt=2.5ps; constraints of C-C bonds; 15~monomers
	(octanoate/sodium) and 1068~water molecules},
  keywords = {membrane; micelle; Ewald boundary condition}
}

@ARTICLE{WIEN88,
  author = {M. C. Wiener and S. Tristram-Nagle and D. A. Wilkinson and L. E.
	Campbell and J. F. Nagle},
  title = {Specific volumes of lipids in fully hydrated bilayer dispersions},
  journal = BBA,
  year = {1988},
  volume = {938},
  pages = {135--143},
  annote = {more methodic paper on how to experimentally determine the specific
	volumes; partial specific volume is defined as incremental change
	in volume per gram added solute; experimental paper; in biological
	systems there is always excess water present, here too; error analysis
	of possible experimental errors; 15 water / lipid in gel phase; 25
	water\lipid in fluid phase; 45A^3 change in specific volume at gel
	melting temperature for DPPC; main transition temperature for DPPC
	@ 42C; pre-transition @ 36C; good table with transition temperatures
	for 7 different phases of DPPC; equilibration time for hydration
	about 30mins; for DLPE @ 35C specific volume=0.942ml\g for F (fluid)
	phase and 0.896ml\g @ 20C for G (gel) phase; graph of specific volumes
	for DPPC},
  keywords = {lipid; absolute specific volume; bilayer; molecular volume; hydration;
	specific volume; DPPC; DLPE; membrane}
}

@ARTICLE{WOLB88,
  author = {C. Wolberger and Y. Dong and M. Ptashne and S. C. Harrison},
  title = {Structure of a phage~434 Cro/{DNA} Complex},
  journal = NAT,
  year = {1988},
  volume = {335},
  pages = {789--795}
}

@ARTICLE{WON88,
  author = {Y. Won and R. A. Friesner},
  title = {Simulation of Optical Spectra from Reaction Center of {\em Rhodopseudomonas
	viridis}},
  journal = JPC,
  year = {1988},
  volume = {92},
  pages = {2208--2214}
}

@INCOLLECTION{ZINT88,
  author = {W. Zinth and J. Dobler and M. A. Franz and W. Kaiser},
  title = {The Primary Steps of Photosynthesis in Bacteriorhodopsin},
  booktitle = {Spectroscopy of Biological Molecules -- New Advances},
  publisher = {Wiley},
  year = {1988},
  editor = {E. D. Schmid and F. W. Schneider and F. Siebert},
  pages = {269--274},
  address = {New York}
}

@MISC{CROF90,
  author = {A. R. Crofts},
  title = {SEQANAL package of programs for sequence analysis},
  howpublished = {Biotechnology Center, University of Illinois},
  year = {1987-1990}
}

@MISC{ROBI89,
  author = {H. H. Robinson and A. R. Crofts},
  title = {pdViewer package of programs for viewing structures from the Brookhaven
	Protein Data Bank on IBM PC and compatible computers},
  howpublished = {Biotechnology Center, University of Illinois},
  year = {1987-1989}
}

@BOOK{POUN87,
  title = {A Tutorial Introduction to {OCCAM} Programming},
  publisher = {INMOS},
  year = {1987},
  author = {David Pountain},
  month = APR,
  note = {\#72TDS11500}
}

@MANUAL{GHEE87,
  title = {{IMS~B}004; {IBM~PC} add-in board},
  author = {Stephen Ghee},
  organization = {{INMOS}},
  month = FEB,
  year = {1987},
  note = {Technical note~11, \#72{TCH}01100}
}

@MANUAL{MAY87,
  title = {Communicating processes and occam},
  author = {David May},
  organization = {{INMOS}},
  month = FEB,
  year = {1987},
  note = {Technical note~20, \#72{TCH}02000}
}

@BOOK{MAY87B,
  title = {{OCCAM}2, Language Definition},
  publisher = {INMOS},
  year = {1987},
  author = {David May},
  month = FEB,
  note = {\#72OCC04401, \#72OCC04402}
}

@MANUAL{MAY87A,
  title = {The transputer implementation of occam},
  author = {David May and Roger Shepherd},
  organization = {{INMOS}},
  month = FEB,
  year = {1987},
  note = {Technical note~21, \#72{TCH}02100}
}

@INPROCEEDINGS{Acha87,
  author = {A. Achari and D. Scott and P. Barlow and J.C. Vidal and Z. otwinowski
	and S. Brunie and P.B. Sigler},
  title = {Facing up to membranes: structure/function relationships in phospholipases},
  booktitle = {Cold spring harbor symposia on Quantitative Biology},
  year = {1987},
  pages = {441--452},
  annote = {review}
}

@ARTICLE{ALLE87a,
  author = {J.P. Allen and T.O. Yeates and H. Komiya and D.C. Rees},
  title = {Structure of the reaction center from {{\it {R}hodobacter sphaeroides}}
	{R-26}: the protein subunits},
  journal = {Proc. Natl. Acad. Sci. U.S.A.},
  year = {1987},
  volume = {84},
  pages = {6162--6166}
}

@BOOK{ALLE87,
  title = {Computer Simulation of Liquids},
  publisher = {Oxford University Press},
  year = {1987},
  author = {M. P. Allen and D.~J. Tildesley},
  address = {New York}
}

@BOOK{AlTi87,
  title = {Computer Simulation of Liquids},
  publisher = {Clarendon Press, Oxford},
  year = {1987},
  author = {M.~P. Allen and D.~J. Tildesley},
  address = {New York},
  note = {Reprinted in paperback in 1989 with corrections},
  nremark = {molecular modeling, force field, boundary condition, ensemble sampling,
	molecular dynamics, constrained dynamics, hard spheres, {M}onte {C}arlo
	simulation, grand canonical ensemble, neighbour list, Ewald summation,
	molecular mechanics, introduction}
}

@ARTICLE{ASHK87,
  author = {A. Ashkin and J. M. Dziedzic and T. Yamane},
  title = {FIXME},
  journal = NAT,
  year = {1987},
  volume = {330},
  pages = {769}
}

@ARTICLE{AUER87,
  author = {J. Auerbach and W. Paul and A. F. Bakers},
  title = {A Special Purpose Computer for Molecular Dynamics: Motivation, Design,
	Implementation, and Application},
  journal = JPC,
  year = {1987},
  volume = {91},
  pages = {4881}
}

@ARTICLE{BAAS87,
  author = {T. Baasov and N. Friedmann and M. Sheves},
  title = {Factors Affecting the {C=N} Stretching in Protonated Retinal {Schiff}-Base\
	--\ A Model Study for Bacteriorhodopsin and Visual Pigments},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {3210--3217}
}

@ARTICLE{BADE87,
  author = {G. Bader and U. Ascher},
  title = {A new basis implementation for a mixed order boundary value {ODE}
	solver},
  journal = SJSSC,
  year = {1987},
  volume = {8},
  pages = {483--500}
}

@ARTICLE{BaHa87,
  author = {Bae and Haug},
  title = {A Recursive Formulation for Constrained Mechanical System Dynamics:
	Part I. Open Loop Systems},
  journal = {Mech.\ Struct and Mach.},
  year = {1987},
  volume = {15},
  pages = {359--382},
  nremark = {fast algorithm for use of internal coordinates for multibody dynamics}
}

@ARTICLE{BAE87,
  author = {Bae, D.-S. and Haug, E. J.},
  title = {A recursive formulation for constrained mechanical system dynamics:
	Part I. Open loop systems},
  journal = {Mech. Struct. \& Mach.},
  year = {1987},
  volume = {15},
  pages = {359--382}
}

@ARTICLE{BaBr87,
  author = {D. Bai and A. Brandt},
  title = {Local mesh refinement multilevel techniques},
  journal = SJSSC,
  year = {1987},
  volume = {8},
  pages = {109--134}
}

@INCOLLECTION{BALD87,
  author = {Robert L.\ Baldwin and David Eisenberg},
  title = {Protein Stability},
  booktitle = {Protein Engineering},
  publisher = {Alan R.\ Liss, Inc.},
  year = {1987},
  editor = {D.\ Oxender},
  pages = {127--148},
  address = {New York}
}

@ARTICLE{BENN87,
  author = {M. K. Bennet and M. B. Kennedy},
  title = {Deduced primary structure of the $\beta$ subunit of brain type {II}
	{Ca$^{2+}$}/calmodulin dependent protein kinase determined by molecular
	cloning},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {1794--1798}
}

@ARTICLE{BERE87,
  author = {H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma},
  title = {The Missing Term in Effective Pair Potentials},
  journal = JPC,
  year = {1987},
  volume = {91},
  pages = {6269--6271},
  annote = {diffusion constant of water @ 300K: D = 2.4*10^-5 cm^2s^-1 and @
	307K: D = 2.7*10^-5 cm^2s^-1},
  keywords = {water simulation; polarizability}
}

@ARTICLE{BERG87,
  author = {M. J. Berger and S. H. Bokhari},
  title = {A Partitioning Strategy for Nonuniform Problems on Multiprocessors},
  journal = {IEEE Transactions on Computers},
  year = {1987},
  volume = {C-36},
  pages = {570--580},
  number = {5}
}

@ARTICLE{Beyn87,
  author = {W.-J. Beyn},
  title = {On the Numerical Approximation of Phase Portraits near Stationary
	Points},
  journal = SJNA,
  year = {1987},
  volume = {24},
  pages = {1095--1113}
}

@ARTICLE{BIAL87,
  author = {William Bialek},
  title = {Physical Limits to Sensation and Perception},
  journal = {Ann.~Rev.~Biophys.~Biophys.~Chem.},
  year = {1987},
  volume = {16},
  pages = {455--478}
}

@ARTICLE{BIRG87,
  author = {R. R. Birge and L. P. Murray and R. Zidovetzki and H. M. Knapp},
  title = {Two-Photon, $^{13}${C} and Two-Dimensional $^{1}${H} {NMR} Spectroscopic
	Studies of Retinyl {Schiff} Bases, Protonated {Schiff} Bases, and
	{Schiff} Base Salts: Evidences for a Protonation Induced $\Pi\Pi^{\star}$
	Excited State Level Ordering Reversal},
  journal = JACS,
  year = {1987},
  volume = {109},
  pages = {2090--2101}
}

@ARTICLE{BiFr87,
  author = {M. Bishop and S. Frinks},
  title = {Error Analysis in Computer Simulations},
  journal = {J. Chem.\ Phys.},
  year = {1987},
  volume = {87},
  pages = {3675--3676}
}

@ARTICLE{BLUN87,
  author = {Blundell, T. L. and Sibanda, B. L. and Sternberg, M. J. E. and Thornton,
	J. M.},
  title = {Knowledge-based prediction of protein structures and the design of
	novel molecules},
  journal = NAT,
  year = {1987},
  volume = {326},
  pages = {347--352}
}

@ARTICLE{BONA87,
  author = {V. Bonacic-Koutecky and K. Schoffel and J. Michl},
  title = {Critically heterosymmetric biradicaloid geometries of the protonated
	Schiff bases},
  journal = TCA,
  year = {1987},
  volume = {72},
  pages = {459--474}
}

@ARTICLE{BRAI87,
  author = {M. S. Braiman and P. L. Ahl and K. J. Rothschild},
  title = {Millisecond {Fourier}-Transform Infrared Difference Spectra of Bacteriorhodopsin's
	{M$_{412}$} Photoproduct},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {5221--5225}
}

@ARTICLE{BrKa87,
  author = {R. E. Bruccoleri and M. Karplus},
  title = {Prediction of the Folding of Short Polypeptide Segments by Uniform
	Conformational Sampling},
  journal = {Biopolymers},
  year = {1987},
  volume = {26},
  pages = {137--168}
}

@ARTICLE{BRYN87,
  author = {J. D. Bryngelson and P. G. Wolynes},
  title = {Spin glasses and the statistical mechanics of protein folding},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {7524--7528}
}

@ARTICLE{BRUN87a,
  author = {A. Br{\"u}nger and J. Kuriyan and M. Karplus},
  title = {Crystallographic {$R$} Factor Refinement by Molecular Dynamics},
  journal = SCI,
  year = {1987},
  volume = {235},
  pages = {458--460}
}

@ARTICLE{BRUN87b,
  author = {A. T. Br{\"u}nger and R. L. Campbell and G. M. Clore and A. M. Gronenborn
	and M. Karplus and G. A. Petsko and M. M. Teeter},
  title = {Solution of a Protein Structure with a Model Obtained from {NMR}
	Interproton Distance Restraints},
  journal = SCI,
  year = {1987},
  volume = {235},
  pages = {1049}
}

@ARTICLE{BUHM87,
  author = {Joachim Buhmann and Robert Divko and Helge Ritter and Klaus Schulten},
  title = {{Physik und Gehirn --- Wie dynamische Modelle von Nervennetzen nat\"urliche
	Intelligenz erkl\"aren}},
  journal = MCM,
  year = {1987},
  volume = {9},
  pages = {108--120}
}

@ARTICLE{BUHM86C,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Influence of Noise on the function of a ``Physiological'' Neural
	Network},
  journal = BC,
  year = {1987},
  volume = {56},
  pages = {313--327}
}

@ARTICLE{BUHM87A,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Noise-Driven Temporal Association in Neural Networks},
  journal = EPL,
  year = {1987},
  volume = {4},
  pages = {1205--1209},
  number = {10}
}

@BOOK{Butc87,
  title = {The Numerical Analysis of Ordinary Differential Equations},
  publisher = {John Wiley and Sons},
  year = {1987},
  author = {J. C. Butcher}
}

@ARTICLE{CARL87,
  author = {Marie-France Carlier and Dominique Pantaloni and Edward D. Korn},
  title = {The Mechanism of {ATP} Hydrolysis Accompanying the Polymerization
	of {Mg}-actin and {Ca}-actin},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {3052--3059}
}

@BOOK{CEVC87,
  title = {Phospholipid Bilayers: Physical Principles and Models},
  publisher = {John Wiley \& Sons},
  year = {1987},
  author = {Gregor Cevc and Derek Marsh},
  address = {New York},
  keywords = {bilayer lipid membranes, phopholipids}
}

@ARTICLE{CHAD87,
  author = {B.~W.~Chadwick and C.~Zhang and R.~J.~Cogdell and H.~A.~Frank},
  title = {The effects of lithium dodecyl sulfate and sodium borohydride on
	the absorption spectrum of the B800-850 light harvesting complex
	from {\em Rhodopseudomonas acidophila} 7750},
  journal = BBA,
  year = {1987},
  volume = {893},
  pages = {444--457}
}

@BOOK{Chan87,
  title = {Introduction to Modern Statistical Mechanics},
  publisher = {Oxford University Press},
  year = {1987},
  author = {D.~Chandler}
}

@ARTICLE{ChMM87,
  author = {J. Chang and J.H. Musser and H. McGregor},
  title = {{PLA$_2$}: Function and pharmacological regulation},
  journal = {Biochem. Pharmacol.},
  year = {1987},
  volume = {36},
  pages = {2429--2436}
}

@ARTICLE{COGD87,
  author = {R. J. Cogdell and H. A. Frank},
  title = {How Carotenoids Function in Photosynthetic Bacteria},
  journal = BBA,
  year = {1987},
  volume = {895},
  pages = {63--79}
}

@ARTICLE{Coop87,
  author = {G.J. Cooper},
  title = {Stability of {R}unge-{K}utta methods for trajectory problems},
  journal = {IMA J. Numer. Anal.},
  year = {1987},
  volume = {7},
  pages = {1--13}
}

@INPROCEEDINGS{CREM87,
  author = {G. Cremer-Bartels and K. Krause},
  title = {Retinal Pteridines},
  booktitle = {Advances in the Biosciencs, Vol. 62, Research in Retinitis Pigmentosa;
	4th Congress of the International Retinitis Association, Part 1,
	Bad Nauheim, West Germany, May 10-13, 1986},
  year = {1987},
  editor = {E. Zrenner and H. Krastel and H. H. Goebel},
  pages = {291--302},
  address = {New York},
  publisher = {Pergamon Press}
}

@BOOK{CUSA87,
  title = {The Physics of Structurally Disordered Matter},
  publisher = {Adam Hilger},
  year = {1987},
  author = {N. E. Cusack},
  address = {Bristol}
}

@BOOK{DEIS87,
  title = {The crystal structure of the photosynthetic reaction center from
	{\it Rhodopseudomonas viridis}},
  publisher = {Plenum Press},
  year = {1987},
  editor = {J. Breton and A. Vermeglio},
  author = {J. Deisenhofer and H. Michel},
  pages = {1--3},
  series = {The photosynthetic bacterial reaction center: Structure and dynamics},
  address = {London}
}

@ARTICLE{DIST87,
  author = {D. L. DiStefano and A. J. Wand},
  title = {Two Dimensional $^1${H NMR} Study of Human Ubiquitin: {A} Main Chain
	Directed Assignment and Structure Analysis},
  journal = {Biochemistry},
  year = {1987},
  volume = {26},
  pages = {7272--7281}
}

@ARTICLE{DKPR87,
  author = {S. Duane and A. D. Kennedy and B. J. Pendleton and D. Roweth},
  title = {Hybrid {M}onte {C}arlo},
  journal = {Phys. Lett. B},
  year = {1987},
  volume = {195},
  pages = {216--222}
}

@ARTICLE{DURN87,
  author = {R. Durbin and D. Willshaw},
  title = {An Analogue Approch to the Travelling Salesman Problem Using an Elastic
	Net Method},
  journal = NAT,
  year = {1987},
  volume = {326},
  pages = {689--691}
}

@ARTICLE{ECKE87,
  author = {Peter Eckelmann},
  title = {{T}ransputer der 2.~{G}eneration},
  journal = {Elektronik},
  year = {1987},
  note = {issue 1, 2, and 3}
}

@ARTICLE{EDHO87,
  author = {O. Edholm and J. Johansson},
  title = {Lipid Bilayer Polypeptide Interactions Studied by Molecular Dynamics
	Simulation},
  journal = EBJ,
  year = {1987},
  volume = {14},
  pages = {203--209},
  annote = {polypeptide alpha-helix inserted; temp (330K) above LC; central question
	of different properties of boundary lipids; dt=5fs; 32 lipids in
	each layer; 75ps runs; negative pressure values; gives usable formulas
	and explanations},
  keywords = {polypeptide; glycophorin; lipid bilayer; molecular dynamics; order
	parameters; lateral diffusion; membrane}
}

@ARTICLE{ENGL87,
  author = {A.R. Engelmann and C.M. Llanos and P.G. Nyholm and O. Tapia and I.
	Pascher},
  title = {Studies on membrane hydration. Part I. {M}onte {C}arlo Simulation
	of the Choletral-Water Interface},
  journal = {Journal of molecular structure},
  year = {1987},
  volume = {151},
  pages = {81--102},
  annote = {Stiudies of choletral membrane}
}

@ARTICLE{ENGE87,
  author = {A.R. Engelmann and C.M.Medina Llanos and P.G. Nyholm and O. Tapla
	and I. Pascher},
  title = {Studies on membrane hydration. Part 1. {M}onte {C}arlo simulation
	of the cholesterol--water interface},
  journal = {J. of Mol. Struct. (Theochem)},
  year = {1987},
  volume = {151},
  pages = {81--102}
}

@ARTICLE{ESTE87,
  author = {James E. Estes and Lynn A. Selden and Lewis C. Gershman},
  title = {Tight Binding of Divalent Cations to Monomeric Actin},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {4952--4957}
}

@ARTICLE{FINC87,
  author = {David Fincham},
  title = {Parallel Computers and Molecular Simulation},
  journal = {Molecular Simulation},
  year = {1987},
  volume = {1},
  pages = {1--45},
  number = {1, 2}
}

@BOOK{FINK87,
  title = {Water Movement through Lipid Bilayers, Pores, and Plasma Membranes},
  publisher = {John Wiley \& Sons},
  year = {1987},
  author = {Alan Finkelstein},
  address = {New York},
  keywords = {plasma membranes, bilayer lipid membranes, water, biological transport}
}

@ARTICLE{GILL87,
  author = {P. Gillis and S. H. Koenig},
  title = {Transverse Relaxation of Solvent Protons Induced by Magnetized Spheres:
	Application to Ferritin, Erythocytes, and Magnetite},
  journal = mrm,
  year = {1987},
  volume = {{\bf 5}},
  pages = {323--345},
  brief = {Outer sphere relaxation is explained here. See esp. p328. Also mentions
	example of deoxegenated erythrocytes as compartmentalized tissue
	w/ contrast agent inside (p325).}
}

@ARTICLE{GILS87,
  author = {Michael K.\ Gilson and Kim A.\ Sharp and Barry H.\ Honig},
  title = {Calculating the Electrostatic Potential of Molecules in Solution:
	Method and Error Assessment},
  journal = JCC,
  year = {1987},
  volume = {9},
  pages = {327--335}
}

@ARTICLE{GiSH87,
  author = {M. K. Gilson and K. A. Sharp and B. H. Honig},
  title = {Calculating the electrostatic potential of molecules in solution:
	method and error assessment},
  journal = JCC,
  year = {1987},
  volume = {9},
  pages = {327--335}
}

@ARTICLE{CHAM87,
  author = {S.~Green and P.~Chambon},
  title = {Oestradiol induction of a glucocorticoid--responsive gene by a chimaeric
	receptor},
  journal = NAT,
  year = {1987},
  volume = {325},
  pages = {75--78},
  annote = {swapping of the domains between receptors, ie finger swap, resulting
	in receptors with chimeric function}
}

@ARTICLE{GREEN87,
  author = {S.~Green and P.~Chambon},
  title = {Oestradiol induction of a glucocorticoid--responsive gene by a chimaeric
	receptor},
  journal = {Nature (Lond.)},
  year = {1987},
  volume = {325},
  pages = {75--78}
}

@ARTICLE{GREE87,
  author = {L.~Greengard and V.~Rokhlin},
  title = {A Fast Algorithm for Particle Simulation},
  journal = JCMP,
  year = {1987},
  volume = {73},
  pages = {325--348}
}

@ARTICLE{GrRo87,
  author = {L. Greengard and V. Rokhlin},
  title = {A fast algorithm for particle simulations},
  journal = {J. Comput.\ Phys.},
  year = {1987},
  volume = {73},
  pages = {325--348}
}

@ARTICLE{GRIS87,
  author = {C. B. Grissom and K. O. Willeford and R. T. Wedding},
  title = {Isotope Effect Studies of the Chemical Mechanism of Nicotinamide
	Adenine Dinucleotide Malic Enzyme from \it{Crassula}},
  journal = {Biochemistry},
  year = {1987},
  volume = {26},
  pages = {2594--2596}
}

@MANUAL{GuBe87,
  title = {Gromos-87 manual},
  author = {W. F. van Gunsteren and H. J. C. Berendsen},
  organization = {Biomos BV},
  address = {Nij\-enborgh 4, 9747 AG Groningen, Netherlands},
  year = {1987}
}

@ARTICLE{VaBe87,
  author = {W. F. van Gunsteren and H. J. C. Berendsen},
  title = {A Leap-Frog Algorithm for Stochastic Dynamics},
  journal = {Molecular Simulation},
  year = {1987}
}

@ARTICLE{HACK87,
  author = {Neil R. Hackett and Lawrence J. Stern and Betty H. Chao and K. Anne
	Kronis and H Gobind Khorana},
  title = {Structure-Function Studies on Bacteriorhodopsin. {V}. {E}ffects of
	Amino Acid Substitutions in the Putative Helix F},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {9277--9284}
}

@BOOK{HaNW87,
  title = {Solving Ordinary Differential Equations I: \mbox{N}on-stiff Systems},
  publisher = {Springer-Verlag},
  year = {1987},
  author = {E. Hairer and S. P. N{\o}{r}sett and G. Wanner},
  address = {Berlin}
}

@ARTICLE{HARD87,
  author = {P. A. Hardy},
  title = {Using the {CRAY} to do {M}onte {C}arlo Calculations for Nuclear Magnetic
	Resonance Imaging},
  journal = {The CLSC News},
  year = {1987},
  volume = {1},
  pages = {1--4},
  number = {3},
  keywords = {simulation}
}

@ARTICLE{HERZ87,
  author = {O. Herzberg and J. Moult and M.N.G. James},
  title = {Molecular Structure of Troponin {C} and its Implications for the
	{Ca}$^{2+}$ Triggering of Muscle Contraction},
  journal = {Methods in Enzymology},
  year = {1987},
  volume = {139},
  pages = {610--632}
}

@ARTICLE{HILL87,
  author = {W. D. Hillis and J. Barnes},
  title = {Programming a highly parallel computer},
  journal = NAT,
  year = {1987},
  volume = {326},
  pages = {27}
}

@ARTICLE{HSIE87A,
  author = {{W.-T.} Hsieh and R. D. Wells},
  title = {Influence of negative supercoiling and of the proximity of left-handed
	{Z-DNA} on the {{\it Escherichia coli}} lactose repressor-operator
	interaction},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {14576--14582}
}

@ARTICLE{HWAN87,
  author = {Jenn-Kang Hwang and Arieh Warshel},
  title = {Microscopic Examination of Free-Energy Relationship for Electron
	Transfer in Polar Solvent},
  journal = JACS,
  year = {1987},
  volume = {109},
  pages = {715--720}
}

@ARTICLE{JAIN87,
  author = {M. K. Jain and W. L. C. Vaz},
  title = {Dehydration of the lipid-protein microinterface on binding of phospholipase
	{A}$_2$ to lipid bilayers},
  journal = BBA,
  year = {1987},
  volume = {905},
  pages = {1--8},
  annote = {Anionic vehsicles, observe dehydration of Trp-3 for PLA2 but not
	for pro-PLA2}
}

@ARTICLE{KABA87,
  author = {G. Kabalka and Edward Buonocore and Karl Hubner and Thomas Moss and
	N. Norley and L. Huang},
  title = {Gadolinium-labelled Liposomes, targeted {MR} contrast agnets for
	the liver and the spleen},
  journal = {Radiology},
  year = {1987},
  volume = {{\bf 163}},
  pages = {255--258},
  brief = {Magin says that here is Gd-DTPA attached to the liposome membrane.}
}

@ARTICLE{KANG87,
  author = {Young Kee Kang and George N{\'e}methy and Harold A. Scheraga},
  title = {Free Energies of Hydration of Solute Molecules},
  journal = JPC,
  year = {1987},
  volume = {91},
  pages = {4105--4117}
}

@ARTICLE{KLUG87,
  author = {A.~Klug and D.~Rhodes},
  title = {``Zinc fingers'': a novel protein motif for nucleic acid recognition},
  journal = TIBS,
  year = {1987},
  volume = {12},
  pages = {464--469},
  annote = {classic cys-2-his-2 zinc fingers}
}

@ARTICLE{KOZY87,
  author = {S.~A.~Kozyavkin and S.~M.~Mirkin and B.~R.~Amirikyan},
  title = {The Ionic Strength Dependence of the Cooperativity Factor for {DNA}
	Melting},
  journal = JBSD,
  year = {1987},
  volume = {5},
  pages = {119--126},
  number = {1},
  annote = {measures of melting of d(AT)$_{24}$ d(AT)$_{24}$ as function conc.}
}

@ARTICLE{KGSB87,
  author = {V. Kumar and S. Green and G. Stack and M. Berry and J.-R Jin and
	P. Chambon},
  title = {Functional domains of the human estrogen receptor},
  journal = {Cell},
  year = {1987},
  volume = {51},
  pages = {941--951}
}

@ARTICLE{KUMA87,
  author = {V.~Kumar and S.~Green and G.~Stack and M.~Berry and J.~R.~Jin and
	P.~Chambon},
  title = {Functional domains of the human estrogen receptor},
  journal = {Cell},
  year = {1987},
  volume = {51},
  pages = {941--951},
  annote = {combined with krus86 implies sequence comparisons revealed regions
	with differential homology suggesting domain structure}
}

@BOOK{LAAR87,
  title = {Simulated Annealing: Theory and Application},
  publisher = {D. Reidel},
  year = {1987},
  author = {P. J. M. van Laarhoven and E. H. L. Aarts},
  address = {Dordrecht}
}

@ARTICLE{LiSc87,
  author = {Z. Li and H. A. Scheraga},
  title = {{M}onte {C}arlo-Minimization Approach to the Multiple-Minima Problem
	in Protein Folding},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {6611--6615},
  number = {19}
}

@ARTICLE{ZHEN87,
  author = {Zhenqin Li and H. A. Scheraga},
  title = {{M}onte {C}arlo-Minimization approach to the multiple-minima problem
	in protein folding},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {6611--6615}
}

@ARTICLE{LOHM87,
  author = {K. J. Lohmann and A. O. D. Willows},
  title = {Lunar-Modulated Geomagnetic Orientation by a Marine Mollusk},
  journal = SCI,
  year = {1987},
  volume = {235},
  pages = {331--334}
}

@ARTICLE{MACD87,
  author = {Peter M. Macdonald and Joachim Seelig},
  title = {Calcium Binding to Mixed Phosphatidylglyc\-er\-ol--Phosphatidylcholine
	Bilayers as Studied by Deuterium Nuclear Magnetic Resonance},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {1231--1240},
  annote = {POPC comes very close to natural lipids},
  keywords = {POPC; POPG; membrane; experimental; surface potential}
}

@ARTICLE{MACD87b,
  author = {R.A. Mac{D}onald and S.A. Simon},
  title = {Lipid monolayer and their relationships to bilayers},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {4089--4093}
}

@BOOK{MCCA87,
  title = {Dynamics of Proteins and Nucleic Acids},
  publisher = {Cambridge University Press},
  year = {1987},
  author = {J. A. McCammon and S. C. Harvey},
  address = {Cambridge}
}

@BOOK{McHa87,
  title = {Dynamics of Proteins and Nucleic Acids},
  publisher = {Cambridge University Press},
  year = {1987},
  author = {J. A. McCammon and S. C. Harvey},
  address = {Cambridge},
  nremark = {molecular mechanics, introduction, water structure, hydration, force
	field}
}

@BOOK{MCCL87,
  title = {Explorations in Parallel Distributed Processing},
  publisher = {MIT Press},
  year = {1987},
  author = {J. L. McClelland and D. E. Rumelhart},
  address = {Cambridge, MA.}
}

@ARTICLE{MERZ87,
  author = {M. M. Merzenich and others},
  title = {Variability in Hand Surface Representations in Areas~3b and~1 in
	Adult Owl and Squirrel Monkeys},
  journal = {J. Comp. Neurology},
  year = {1987},
  volume = {258},
  pages = {281--296}
}

@ARTICLE{MICH87,
  author = {H. Michel and J. Deisenhofer},
  title = {The Photosynthetic Reaction Centre from the Purple Bacterium {\it
	Rhodopseudomonas viridis}},
  journal = CS,
  year = {1987},
  volume = {27B},
  pages = {173--180},
  annote = {the only known X-ray structures of membrane proteins are: \Rps, Rhodobacter
	sheroides, porin (and now Bacteriorhodopsin); paper presented by
	H. Michel at the Nobel symposium `Membrane Proteins: Structure, Function,
	Assembly', Karlskoga, Sweden, 1--5 September 1986; they got the Nobel
	price for Chemistry in 1988 for the structure resolution}
}

@ARTICLE{MOGI87,
  author = {Tatsushi Mogi and Lawrence J. Stern and Neil R. Hackett and H. Gobind
	Khorana},
  title = {Bacteriorhodopsin mutants containing single tyrosine to phenylalanine
	substitutions are all active in proton translocation},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {5595--5599}
}

@ARTICLE{NADL87,
  author = {Walter Nadler and Axel Br{\"u}nger and Klaus Schulten and Martin
	Karplus},
  title = {Molecular and Stochastic Dynamics of Proteins},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {7933--7937},
  annote = {uses stochastic boundary simulation}
}

@BOOK{NEWB87,
  title = {Statistics For Business and Economics},
  publisher = {Englewood Cliffs},
  year = {1987},
  author = {Paul Newbold},
  address = {New Jersey},
  annote = {Statistics Tables, etc. from barb}
}

@ARTICLE{ONUC87,
  author = {Jos{\'e} Nelson Onuchic},
  title = {Effect of Friction on Electron The Two Reaction Coordinate Case},
  journal = JCP,
  year = {1987},
  volume = {86},
  pages = {3925--3943}
}

@ARTICLE{OOI87,
  author = {Tatsuo Ooi and Motohisa Oobatake and George N{\'e}methy and Harold
	A.\ Scheraga},
  title = {Accessible surface areas as a measure of the thermodynamic parameters
	of hydration of peptides},
  journal = PNAS,
  year = {1987},
  volume = {84},
  pages = {3086--3090},
  keywords = {free energy; hydration; simulation-methodology}
}

@ARTICLE{PAK87,
  author = {John H. Pak and Vincent P. Bork and Richard E. Norberg and Michael
	H. Creer and Robert A. Wolf and Richard W. Gross},
  title = {Disparate Molecular Dynamics of Plasmenylcholine Bilayers},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {4824--4830},
  annote = {experimental, not simulation; Gross works with Garland Marshall in
	St. Louis}
}

@ARTICLE{PESC87,
  author = {J. Peschke and J. Riegler and H. M{\"o}hwald},
  title = {Quantative analysis of membrane distorsions induced by mismatch of
	protein and lipid hydrophobic thickness},
  journal = {Eur. Biophys. J},
  year = {1987},
  volume = {14},
  pages = {385--391}
}

@ARTICLE{PETR87,
  author = {J. W. Petrich and J. Breton and J. L. Martin and A. Antonetti},
  title = {Femtosecond Absorption Spectroscopy of Light-Adapted and Dark-Adapted
	Bacteriorhodopsin},
  journal = CPL,
  year = {1987},
  volume = {137},
  pages = {369--375}
}

@ARTICLE{PHIL87,
  author = {J. B. Phillips},
  title = {Specialized Visual Receptors Respond to Magnetic Field Alignment
	in the Blowfly},
  journal = {Society for Neuroscience Abstracts},
  year = {1987},
  volume = {13},
  pages = {397},
  number = {1}
}

@ARTICLE{PoRi87,
  author = {J.~W. Ponder and F.~M. Richards},
  title = {An Efficient Newton-like Method for Molecular Mechanics Energy Minimization
	of Large Molecules},
  journal = JCC,
  year = {1987},
  volume = {8},
  pages = {1016--1024},
  annote = {TINKER}
}

@ARTICLE{Qin87,
  author = {M.-Z. Qin},
  title = {A Difference Scheme for the \mbox{Hamiltonian} Equation},
  journal = {J. Comput. Math.},
  year = {1987},
  volume = {5},
  pages = {203--209},
  number = {3}
}

@ARTICLE{SHAS87,
  author = {Shashidar N. Rao and others},
  title = {Free Energy Perturbation Calculations on Binding and Catalysis after
	Mutating Asn 155 in Subtilisin},
  journal = NAT,
  year = {1987},
  volume = {328},
  pages = {551}
}

@ARTICLE{RICH87,
  author = {H.~Richard-Foy and G.~L.~Hager},
  title = {Sequence-specific positioning of nucleosomes over the steroid-inducible
	{MMTV} promoter},
  journal = EMBO,
  year = {1987},
  volume = {6},
  pages = {2321--2328},
  annote = {six positioned nuclesomes}
}

@ARTICLE{RIPS87,
  author = {Ilya Rips and Joshua Jortner},
  title = {Dynamic Solvent Effects on Outer-Sphere Electron Transfer},
  journal = JCP,
  year = {1987},
  volume = {87},
  pages = {2090--2104}
}

@INCOLLECTION{RITT87,
  author = {Helge Ritter and Klaus Schulten},
  title = {Planning a Dynamic Trajectory via Path Finding in Discretized Phase
	Space},
  booktitle = {Parallel Processing: Logic, Organization, and Technology},
  publisher = {Springer},
  year = {1987},
  volume = {253},
  series = {Lecture Notes in Computer Science},
  pages = {29--39}
}

@ARTICLE{ROME87,
  author = {G. Romero and K. Thompson and R. L. Biltonen},
  title = {The activation of Porcine Pancreatic Phospholipase {A}$_2$ by dipalmitoylphosphatidylcholine
	large unilamellar vesicles},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {13476--13482},
  annote = {kinetics}
}

@INCOLLECTION{ROOS87,
  author = {B.~O.~Roos},
  title = {{The Complete Active Space Self-Consistent Field Method and its Applications
	in Electronic Structure Calculations}},
  booktitle = {Advances in Chemical Physics; Ab InitioMethods in Quantum Chemistry-II},
  publisher = {John Wiley and Sons Ltd.},
  year = {1987},
  editor = {K.~P.~Lawley},
  pages = {399--445}
}

@BOOK{RUME87,
  title = {Parallel Distributed Processing, Vol. 1},
  publisher = {MIT Press},
  year = {1987},
  author = {D. E. Rumelhart and J. L. McClelland},
  address = {Cambridge}
}

@ARTICLE{SAIN87,
  author = {S. Saini and D. D. Stark and P. F. Hahn and J. Wittenberg and T.
	J. Brady and J. T. Ferruci},
  title = {Ferrite Particles: A Superparamagnetic {MR} Contrast Agent for the
	Reticuloendothelical System},
  journal = {Radiology},
  year = {1987},
  volume = {{\bf 162}},
  pages = {211--216},
  keywords = {Superparamagnetic Contrast Agent}
}

@ARTICLE{SANG87,
  author = {Bi-Ching Sang and Donald M. Gray},
  title = {fd Gene 5 Protein Binds to Double-Stranded Polydeoxyribonucleotides
	Poly{(dA-dT)} and Poly{[d(A-T-d(A-T)]}},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {7210--7214}
}

@ARTICLE{SaVa87,
  author = {J. M. Sanz-Serna and F. Vadillo},
  title = {Studies of Numerical Nonlinear Instability \mbox{III}: Augmented
	\mbox{Hamiltonian} Systems},
  journal = {SIAM J. Appl. Math.},
  year = {1987},
  volume = {47},
  pages = {92--108},
  number = {1}
}

@ARTICLE{SCHE87,
  author = {John A.\ Schellman},
  title = {The Thermodynamic Stability of Proteins},
  journal = ARBBC,
  year = {1987},
  volume = {16},
  pages = {115--137}
}

@BOOK{SCHN87,
  title = {Comprehensive B$_{12}$: Chemistry, Biochemistry, Nutrition, Ecology,
	and Medicine},
  publisher = {Walter de Gruyter},
  year = {1987},
  author = {Z. Schneider and A. Stroinski},
  address = {Berlin}
}

@ARTICLE{SCHR86,
  author = {M.\ Y.\ Schrier and G.\ Defoster and E.\ E.\ Schrier and M.\ Starzak},
  title = {Enthalpies of Transfer for Proteins from Aqueous to Water-Alcohol
	Solutions: A Test for Models of Residues Exposed to Solvent},
  journal = ARBBC,
  year = {1987},
  volume = {16},
  pages = {115--137}
}

@INCOLLECTION{SCHU87,
  author = {Klaus Schulten},
  title = {{Ordnung aus Chaos, Vernunft aus Zufall --- Physik biologischer und
	digitaler Infor\-mations\-verarbeitung}},
  booktitle = {Ordnung aus dem Chaos},
  publisher = {Piper Verlag},
  year = {1987},
  editor = {B.-O. K{\"u}ppers},
  pages = {243--268},
  address = {Munich}
}

@ARTICLE{SEEL87,
  author = {Joachim Seelig and Peter M. Macdonald},
  title = {Phospholipids and Proteins in Biological Membranes. {$^2$H NMR} as
	a Method To Study Structure, Dynamics, and Interactions},
  journal = ACR,
  year = {1987},
  volume = {20},
  pages = {221--228},
  annote = {nice introduction; membrane surface potential about 10mV; explains
	how D-NMR works; dismisses the idea of special boundary lipids}
}

@ARTICLE{SEEL87A,
  author = {Joachim Seelig and Peter M. Macdonald and Peter G. Scherer},
  title = {Phospholipid Head Groups as Sensors of Electric Charge in Membranes},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {7534--7541},
  number = {24},
  annote = {head groups behave as sensors of the electric charge at the membrane
	surface; head group parallel (within 30^o) to membrane surface; H-bond
	network restricts movement of head groups; POPC closest to natural
	lipid membranes; a change of the charge environment changes somehow
	the orientation of the head group; POPC even without ions around
	*does* have a non-zero surface potential due to the head group dipoles
	which are not completely parallel to the surface},
  keywords = {head group; experimental; membrane; POPC; surface potential},
  suggestions = {investigate head group angle and surface potential}
}

@ARTICLE{SELT87,
  author = {S. Seltzer},
  title = {{MNDO} barrier heights for catalyzed bicycle-pedal, hula twist, and
	ordinary cis-trans isomerizations of protonated retinal {S}chiff
	base},
  journal = JACS,
  year = {1987},
  volume = {109},
  pages = {1627--1631}
}

@ARTICLE{SHAR87,
  author = {Kim Sharp and Richard Fine and Klaus Schulten and Barry Honig},
  title = {{B}rownian Dynamics Simulation of Diffusion to Irregular Bodies},
  journal = PC,
  year = {1987},
  volume = {91},
  pages = {3624--3631},
  annote = {describes a computer program (and simulations done with it) which
	uses table look-up to speed up the computations at the expense of
	large memory requirements; variable (adaptive) time step and max.
	move criterion of 0.5\AA},
  keywords = {Smoluchowski diffusion equation (Brownian dynamics); {M}onte {C}arlo
	algorithm; substrate--enzyme association; superoxide to superoxid
	dismutase (SOD)}
}

@ARTICLE{SHEP87,
  author = {R. Shepard},
  title = {The Multicofiguration Self-Consistent Field Method.},
  journal = ACP,
  year = {1987},
  volume = {69},
  pages = {63--200}
}

@ARTICLE{SMIT87,
  author = {G. S. Smith and C. R. Safinya and D. Roux and N. A. Clark},
  title = {X-ray studies of freely suspended films of a multilamellar lipid
	system},
  journal = MCLC,
  year = {1987},
  volume = {144},
  pages = {235--255},
  annote = {requested Tx=19920908.}
}

@ARTICLE{SMIT87A,
  author = {S. O. Smith and J. A. Pardoen and J. Lugtenburg and R. A. Mathies},
  title = {Vibrational Analysis of the 13-{\it cis}-Retinal Chromophore in Dark-Adapted
	Bacteriorhodopsin},
  journal = JPC,
  year = {1987},
  volume = {91},
  pages = {804--819}
}

@ARTICLE{SOLO87,
  author = {L.R. Solomon and P.A. Rubenstein},
  title = {Studies on the role of actin's {N}-methylhistidine using oligodeoxynucleotide-directed
	site-specific mutagenesis},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {11382--11388}
}

@ARTICLE{STAT87,
  author = {D.~J. States and T. E. Greighton and C. M. Dobson and M. Karplus},
  title = {Conformations of Intermediates in the Folding of the Pancreatic Trypsin
	Inhibitor},
  journal = JMB,
  year = {1987},
  volume = {195},
  pages = {731--739},
  annote = {BPTI}
}

@BOOK{STEI87,
  title = {{OCCAM2}},
  publisher = {H\"uthig-Verlag},
  year = {1987},
  author = {Ralf Steinmetz},
  address = {Heidelberg}
}

@ARTICLE{Suri87,
  author = {Y.~B. Suris},
  title = {Some properties of methods for the numerical integration of systems
	of the form $\ddot{x} = f(x)$},
  journal = {Zh. Vychisl. Mat. i Mat. Fiz.},
  year = {1987},
  volume = {27},
  pages = {1504--1515},
  note = {(in Russian). Same as {\em U.S.S.R. Comput. Maths. Phys.,} 27(5):149-156,
	1987}
}

@ARTICLE{TAVA87,
  author = {Paul Tavan and Klaus Schulten},
  title = {Electronic Excitations in Finite and Infinite Polyenes},
  journal = PRB,
  year = {1987},
  volume = {36},
  pages = {4337--4358},
  number = {8},
  annote = {Sept 15}
}

@ARTICLE{TRAV87,
  author = {A.~A.~Travers},
  title = {{DNA} bending and nucleosome positioning},
  journal = TIBS,
  year = {1987},
  volume = {12},
  pages = {108--112}
}

@ARTICLE{TRIS87,
  author = {H. W. Trissl and W. Gartner},
  title = {Rapid Charge Separation and Bathochromic Absorption Shift of Flash-Excited
	Bacteriorhodopsins Containing 13-Cis or All-Trans Forms of Substituted
	Retinals},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {751--758}
}

@ARTICLE{TUCH87,
  author = {E. Tuchsen and J.M. Hayes and S. Ramaprasad and V. Copie and C. Woodward},
  title = {Solvent exchange of buried water and hydrogen exchange of peptide
	NH groups hydrogen bonded to buried waters in bovine pancreatic trypsin
	inhibitor},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {5163--5172}
}

@BOOK{WAIT87,
  title = {The Phospholipases},
  publisher = {Plenum Press},
  year = {1987},
  author = {Moseley Waite},
  address = {New York},
  edition = {1}
}

@ARTICLE{WANG87,
  author = {A. Wang and G. Ughetto and G. J. Quigley and A. Rich},
  title = {Interactions between an Anthracycline Antibiotic and {DNA}: Molecular
	Structure of Daunomycin Complexed to d(CpGpTpApCpG) at 1.2\,{\AA\
	} Resolution},
  journal = BCH,
  year = {1987},
  volume = {26},
  pages = {1152--1163}
}

@ARTICLE{WERN87,
  author = {H-J. Werner},
  title = {Matrix-Formulated Direct Multiconfiguration Self-Consistent Field
	and Multiconfiguration Reference Configuration-Interaction Methods.},
  journal = ACP,
  year = {1987},
  volume = {69},
  pages = {1--62}
}

@ARTICLE{WEST87,
  author = {E.~Westhof},
  title = {Re-refinement of the {B}-dodecamer d({CGCGAATTCGCG})$_2$ with a comparative
	analysis of the solvent in it and in the {Z}-hexamer {5--BR--CG5--BR--CG5--BR--CG}},
  journal = JBSD,
  year = {1987},
  volume = {5},
  pages = {581}
}

@ARTICLE{WHIT87A,
  author = {S.P. White and C. Cohen and G.N. Jr. Phillips},
  title = {Structure of co-crystals of tropomyosin and troponin},
  journal = NAT,
  year = {1987},
  volume = {325},
  pages = {826--8}
}

@ARTICLE{WHIT87,
  author = {Stephen H. White and Russell E. Jacobs and Glen I. King},
  title = {Partial specific volumes of lipid and water in mixtures of egg lecithin
	and water},
  journal = BJ,
  year = {1987},
  volume = {52},
  pages = {663--665},
  annote = {specific volumes of water and lipid close to 1cm^3\g; lecithin=phosphatidylcholine;
	specific volumes also depending on the relative humidity (RH)=P\P_0
	(P: vapor pressure of water in mixture, P_0: vapor pressure of pure
	water), also called water activity; not very high precision experiments},
  keywords = {DOPC; membrane; liposomes}
}

@ARTICLE{WHIT87B,
  author = {P. A. Whitson and {W.-T.} Hsieh and R. D. Wells and K. S. Mathews},
  title = {Supercoiling facilitates {\it lac} operator-repressor-pseudooperator
	interactions},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {4943--4946}
}

@ARTICLE{WHIT87C,
  author = {P. A. Whitson and {W.-T.} Hsieh and R. D. Wells and K. S. Mathews},
  title = {Influence of supercoiling and sequence context on operator {DNA-binding}
	with {\it lac} repressor},
  journal = JBC,
  year = {1987},
  volume = {262},
  pages = {14592--14599}
}

@ARTICLE{WOLY87,
  author = {Peter G. Wolynes},
  title = {Dissipation, Tunneling and Adiabaticity Criteria for Curve Crossing
	Problems in the Condenced Phase},
  journal = JCP,
  year = {1987},
  volume = {86},
  pages = {1957--1966}
}

@ARTICLE{ZACC87,
  author = {G. Zacca\"{\i}},
  title = {Structure and Hydration of Purple Membranes in Different Conditions},
  journal = JMB,
  year = {1987},
  volume = {194},
  pages = {569--572}
}

@TECHREPORT{Zhao87,
  author = {Feng Zhao},
  title = {An {O(N)} Algorithm for Three-Dimensional {N}-Body Simulations},
  institution = {{MIT} Artificial Intelligence Laboratory},
  year = {1987},
  number = {995}
}

@ARTICLE{ZVEL87,
  author = {M. J. Zvelebil and G. J. Barton and W. R. Taylor and M. J. Sternberg},
  title = {Prediction of Protein Secondary Structure and Active Sites using
	the Alignment of Homologous Sequences},
  journal = JMB,
  year = {1987},
  volume = {195},
  pages = {957}
}

@INPROCEEDINGS{FeQi86,
  author = {K. Feng and M.-Z. Qin},
  title = {The Symplectic Methods for Computation of \mbox{Hamiltonian} Equations},
  booktitle = {Proc. of 1st Chinese Conf. on Numerical Methods of PDEs},
  year = {1986},
  pages = {1--37},
  address = {Shanghai, China},
  month = MAR
}

@ARTICLE{VAND86,
  author = {R. {van der Steen} and P. L. Biesheuvel and P. L. Mathies and J.
	Lugtenburg},
  title = {Retinal Analogs with Locked 6-7 Conformations Show That Bacteriorhodopsin
	Requires the 6-s-{\it trans} Conformation of the Chromophore},
  journal = JACS,
  year = {1986},
  volume = {108},
  pages = {6410--6411}
}

@ARTICLE{AbKh86,
  author = {David M. Abercrombie and H. Gobind Khorana},
  title = {Regeneration of Native Bacteriorhodopsin Structure Following Acetylation
	of $\epsilon$-Amino Groups of Lys-30, -40, and -41},
  journal = JBC,
  year = {1986},
  volume = {261},
  pages = {4875--4880}
}

@ARTICLE{AGUA86,
  author = {James B. Aguayo and Stephen J. Blackband and Joseph Schoeniger and
	Mark A. Mattingly and Markus Hintermann},
  title = {Nuclear magnetic resonance imaging of a single cell},
  journal = NAT,
  year = {1986},
  volume = {322},
  pages = {190}
}

@BOOK{AhSU86,
  title = {Compilers: Principles, Techniques, and Tools},
  publisher = {Addison-Wesley},
  year = {1986},
  author = {A. V. Aho and R. Sethi and J. D. Ullman},
  address = {Reading}
}

@ARTICLE{AlNM86,
  author = {S. A. Allison and S. H. Northrup and J. A. McCammon},
  title = {Simulation of biomolecular diffusion and complex formation},
  journal = {Biophys.\ J.},
  year = {1986},
  volume = {49},
  pages = {167--175},
  number = {1}
}

@ARTICLE{Ande86,
  author = {C. R. Anderson},
  title = {A Method of Local Corrections for Computing the Velocity Field Due
	to a Distribution of Vortex Blobs},
  journal = {J. Comput.\ Phys.},
  year = {1986},
  volume = {62},
  pages = {111--123}
}

@ARTICLE{ANGE86,
  author = {A. Angerhofer and R.J. Cogdell and M.F. Hipkins},
  title = {A spectral characterization of the light-harvesting pigment-protein
	complexes from {\em {R}hodopseudomonas acidophila}},
  journal = {Biochim.~Biophys.~Acta},
  year = {1986},
  volume = {848},
  pages = {333--341}
}

@ARTICLE{ARGO86,
  author = {P. Argos and J.~K.~M. Rao},
  title = {Prediction of protein structure},
  journal = ME,
  year = {1986},
  volume = {130},
  pages = {185--210}
}

@ARTICLE{BAAS86,
  author = {T. Baasov and M. Sheves},
  title = {Alteration of {pK}$_{{\rm a}}$ of the Bacteriorhodopsin Protonated
	{Schiff} Base. \ {A} Study With Model Compounds},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {5249--5258}
}

@ARTICLE{BaHu86,
  author = {J. Barnes and P. Hut},
  title = {A Hierarchical ${O}({N}\log {N})$ Force-Calculation Algorithm},
  journal = NAT,
  year = {1986},
  volume = {324},
  pages = {446--449}
}

@ARTICLE{BELA86,
  author = {M.L. Belaya and M.V. Feigel'man and V.G. Levadny},
  title = {Hydration forces as a result of non-local water polarizability},
  journal = {Chem.\ Phys.\ Lett.},
  year = {1986},
  volume = {126},
  pages = {361--364}
}

@ARTICLE{Bent86,
  author = {J. Bentley},
  title = {Little Languages},
  journal = {Communications of the ACM},
  year = {1986},
  volume = {29},
  pages = {711--721},
  number = {8}
}

@INPROCEEDINGS{BERE86,
  author = {H.~J.~C. Berendsen and W.~F.~van Gunsteren},
  title = {Practical Algorithms for Dynamic Simulations},
  booktitle = {Proceedings of the International School of Physics, ``Enrico Fermi''},
  year = {1986},
  editor = {G. C. Ciccotti and W. G. Hoover},
  volume = {on course~97},
  pages = {43--65},
  address = {Amsterdam},
  publisher = {North-Holland},
  annote = {order of integrator should be at least 3 because of systematic sign
	of second potential derivative},
  chapter = {Molecular Dynamics Simulation of Statistical Mechanical Systems},
  keywords = {SHAKE, algorithms: Gear, Euler, Verlet, Beeman, constraints, stochastic
	dynamics, cut-off schemes, polarizability, coupling to heat bath/pressure}
}

@ARTICLE{BINN86,
  author = {G. Binning and C. F. Quate and G. Gerber},
  title = {Atomic force microscope},
  journal = PRL,
  year = {1986},
  volume = {56},
  pages = {930--933},
  annote = {june 1}
}

@INCOLLECTION{BITT86,
  author = {Robert Bittl and Klaus Schulten},
  title = {Study of Polymer Dynamics by Magnetic Field Dependent Biradical Reactions},
  booktitle = {Biophysical Effects of Steady Magnetic Fields},
  publisher = {Springer},
  year = {1986},
  editor = {G. Maret and N. Boccara and J. Kiepenheuer},
  volume = {11},
  series = {Proceedings in Physics},
  pages = {90--98},
  address = {Berlin}
}

@ARTICLE{BIXO86,
  author = {Mordechai Bixon and Joshua Jortner},
  title = {Coupling of Protein Modes to Electron Transfer in Bacterial Photosynthesis},
  journal = JPC,
  year = {1986},
  volume = {90},
  pages = {3795--3800}
}

@ARTICLE{BLAS86,
  author = {G. G. Blasdel and G. Salama},
  title = {Voltage Sensitive Dyes Reveal a Modular Organization in Monkey Striate
	Cortex},
  journal = NAT,
  year = {1986},
  volume = {321},
  pages = {579--585}
}

@ARTICLE{BOGU86,
  author = {Mark. S. Boguski and Mark Freeman and Nabil A. Elshourbagy and John
	M. Taylor and Jeffrey I. Gordon},
  title = {On computer-assisted analysis of biological sequences: proline punctuation,
	consensus sequences, and apolipoprotein repeats},
  journal = JLR,
  year = {1986},
  volume = {27},
  pages = {1011--1034}
}

@INCOLLECTION{BUHM86D,
  author = {Joachim Buhmann and Robert Divko and Helge Ritter and Klaus Schulten},
  title = {Physicists Explore Human and Artificial Intelligence},
  booktitle = {Structure and Dynamics of Nucleic Acids, Proteins and Membranes},
  publisher = {Plenum Press},
  year = {1986},
  pages = {301--328},
  ediotr = {E. Clementi and S. Chin}
}

@ARTICLE{BUHM86,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Associative Recognition and Storage in a Model Network of Physiological
	Neurons},
  journal = BC,
  year = {1986},
  volume = {54},
  pages = {319--335}
}

@INCOLLECTION{BUHM86A,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {A Physiological Neural Network as an Autoassociative Memory},
  booktitle = {Disordered Systems and Biological Organization},
  publisher = {Springer},
  year = {1986},
  editor = {E. Bienenstock and F. Fogelman and G. Weisbuch},
  pages = {273--279}
}

@INPROCEEDINGS{BUHM86B,
  author = {Joachim Buhmann and Klaus Schulten},
  title = {Influence of Noise on the Behaviour of an Autoassociative Neural
	Network},
  booktitle = {Neural Networks for Computing},
  year = {1986},
  editor = {J. S. Denker},
  pages = {71--76},
  publisher = {American Institute of Physics Publication, Conference Proceedings
	151},
  annote = {This conference took place in Snowbird, Utah.}
}

@ARTICLE{CARL86,
  author = {Marie-France Carlier and Dominique Pantaloni and Edward D. Korn},
  title = {Fluorescence Measurements of the Binding of Cations to High-affinity
	and Low-affinity Sites on {ATP-G}-actin},
  journal = JBC,
  year = {1986},
  volume = {261},
  pages = {10778--10784}
}

@ARTICLE{CARL86A,
  author = {Marie-France Carlier and Dominique Pantaloni and Edward D. Korn},
  title = {The Effects of {Mg}$^{2+}$ at the High-affinity and Low-affinity
	Sites on the Polymerization of Actin and Associated {ATP} Hydrolysis},
  journal = JBC,
  year = {1986},
  volume = {261},
  pages = {10785--10792}
}

@ARTICLE{CHOT86,
  author = {C. Chothia and A. M. Lesk},
  title = {The relation between the divergence of sequence and structure in
	proteins},
  journal = EMBO,
  year = {1986},
  volume = {5},
  pages = {823--826}
}

@ARTICLE{COHE86,
  author = {F. E. Cohen and R. M. Abarbanel and I. D. Kuntz and R. J. Fletterick},
  title = {Turn Prediction in Proteins using a Pattern-Matching Approach},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {266}
}

@BOOK{COX86,
  title = {Object Oriented Programming},
  publisher = {Addison-Wesley},
  year = {1986},
  author = {Brad J. Cox},
  address = {New York}
}

@ARTICLE{CROU86,
  author = {Rosalie K. Crouch},
  title = {Studies of Rhodopsin and Bacteriorhodopsin Using Modified Retinals},
  journal = PCPB,
  year = {1986},
  volume = {44},
  pages = {803--807}
}

@ARTICLE{DALL86,
  author = {William J. Dally and Charles L. Seitz},
  title = {The torus routing chip},
  journal = DC,
  year = {1986},
  volume = {1},
  pages = {187--196},
  annote = {deadlock avoidance scheme: spiral},
  keywords = {VLSI; Interconnection networks; communication networks; concurrent
	computation; parallel processing; deadlock-free routing; self-timed
	logic; asynchronous logic; message passing multiprocessors}
}

@BOOK{DAWS86,
  title = {Data for Biochemical Research},
  publisher = {Clarendon Press},
  year = {1986},
  author = {R.M.C. Dawson and D.C. Elliott and W.H. Elliott and K.M. Jones},
  address = {Oxford}
}

@INPROCEEDINGS{DIVK86,
  author = {Robert Divko and Klaus Schulten},
  title = {Stochastic Spin Models for Pattern Recognition},
  booktitle = {Neural Networks for Computing},
  year = {1986},
  editor = {J. S. Denker},
  pages = {129--134},
  publisher = {American Institute of Physics Publication, Conference Proceedings
	151},
  annote = {This conference took place in Snowbird, Utah.}
}

@ARTICLE{DZHA86,
  author = {P.G. Dzhavakhidze and A.A. Kornyshev and V.K. Levadny},
  title = {The role of the interface in the nonlocal electrostatic theory of
	hydration force},
  journal = {Phys. Lett. A},
  year = {1986},
  volume = {118},
  pages = {203--208}
}

@ARTICLE{EARN86,
  author = {T. N. Earnest and P. Roepe and M. S. Braiman and J. Gillespie and
	K. J. Rothschild},
  title = {Orientation of the Bacteriorhodopsin Chromophore Probed by Polarized
	{Fourier}-Transform Infrared Difference Spectroscopy},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {7793--7798}
}

@ARTICLE{EDBE86,
  author = {Roger Edberg and Denis J. Evans and G. P. Morriss},
  title = {Constrained molecular dynamics: Simulations of liquid alkanes with
	a new algorithm},
  journal = JCP,
  year = {1986},
  volume = {84},
  pages = {6933--6939},
  number = {12},
  annote = {Gives good ideas on how to analyze thermodynamics properties. Very
	theoretical. Not a general alternative to SHAKE.}
}

@ARTICLE{EISE86,
  author = {David Eisenberg and Andrew D.\ McLachlan},
  title = {Solvation energy in protein folding and binding},
  journal = NAT,
  year = {1986},
  volume = {319},
  pages = {199--203}
}

@ARTICLE{ENGE86,
  author = {Engelman, D. M. and Steitz, T. A. and Goldman, A.},
  title = {Identifying nonpolar transbilayer helices in amino acid sequences
	of membrane proteins},
  journal = {Ann. Rev. Biophys. Biophys. Chem.},
  year = {1986},
  volume = {15},
  pages = {321--353}
}

@ARTICLE{Feng86,
  author = {K. Feng},
  title = {Difference Schemes for \mbox{ Hamiltonian} Formalism and Symplectic
	Geometry},
  journal = {J. Comput. Math.},
  year = {1986},
  volume = {4},
  pages = {279--289},
  number = {3}
}

@ARTICLE{FLEW86,
  author = {R.F. Flewelling and W.L. Hubbell},
  title = {Hydrophobic ion interactions with membranes. Thermodynamics analysis
	of tetraphenylphosphonium binding to vesicles},
  journal = BJ,
  year = {1986},
  volume = {49},
  pages = {531--540}
}

@ARTICLE{FREE86,
  author = {Freedman, K A and Becker, R S},
  title = {Comparative investigation of the photoisomerization of the protonated
	and unprotonated n-butylamine {Schiff} bases 9-cis, 11-cis, and all-trans-retinals},
  journal = {J. Am. Chem. Soc.},
  year = {1986},
  volume = {108},
  pages = {1245--1251}
}

@ARTICLE{GaVa86,
  author = {D. Gannon and J. Vanrosendale},
  title = {On The Structure of Parallelism in a Highly Concurrent {PDE} Solver},
  journal = JPDC,
  year = {1986},
  volume = {3},
  pages = {106--135},
  number = {1}
}

@ARTICLE{Gear86,
  author = {C. W. Gear},
  title = {Maintaining Solution Invariants in the Numerical Solution of \mbox{ODEs}},
  journal = SJSSC,
  year = {1986},
  volume = {7},
  pages = {734--743},
  number = {3}
}

@ARTICLE{GERW86,
  author = {K. Gerwert and F. Siebert},
  title = {Evidence for Light-Induced 13-{\it cis} 14-s-{\it cis} Isomerization
	in Bacteriorhodopsin Obtained by {F}ourier Transform {IR} Difference
	Spectrometry},
  journal = EMBO,
  year = {1986},
  volume = {4},
  pages = {805--812}
}

@ARTICLE{GLAE86,
  author = {Glaeser,R.M. and Baldwin,J. and Ceska,T. A. and Henderson,R.},
  title = {Electron diffraction analysis of the {M}$_{412}$ intermediate of
	bacteriorhodopsin},
  journal = BJ,
  year = {1986},
  volume = {50},
  pages = {913--920}
}

@ARTICLE{GOER86,
  author = {H. Goerrissen and D. Marsh and A. Rietveld and B. de Kruijff},
  title = {Apocytochrome C binding to negatively charged lipid dispersions studied
	by spin-label electron spin resonance},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {2904--2901}
}

@ARTICLE{GrSa86,
  author = {D.F.\ Griffiths and J.M.\ Sanz-Serna},
  title = {On the Scope of the Method of Modified Equations},
  journal = SJSSC,
  year = {1986},
  volume = {7},
  pages = {994--1008}
}

@ARTICLE{GRIN86,
  author = {A. Grinvald and E. Lieke and R. D. Frostig and C. D. Gilbert and
	T. N. Wiesel},
  title = {Functional Architecture of Cortex Revealed by Optical Imaging Technique},
  journal = NAT,
  year = {1986},
  volume = {324},
  pages = {361}
}

@ARTICLE{HENR86,
  author = {E.R. Henry and W.R. Eaton and R.M. Hochstrasser},
  title = {Molecular Dynamics Simulations of Cooling in Laser-excited Heme Proteins},
  journal = PNAS,
  year = {1986},
  volume = {83},
  pages = {8982--8986}
}

@ARTICLE{HERZ86,
  author = {O. Herzberg and J. Moult and M.N.G. James},
  title = {A Model for the {Ca}$^{2+}$ - induced Conformational Transition of
	Troponin {C}},
  journal = {J. Biol. Chem.},
  year = {1986},
  volume = {261},
  pages = {2638--2644}
}

@ARTICLE{HONI86,
  author = {B. H. Honig and W. L. Hubbell and R. F. Flewelling},
  title = {Electrostatic interactions in membranes and proteins},
  journal = {Ann. Rev. Biophys. Biophys. Chem.},
  year = {1986},
  volume = {15},
  pages = {163--193},
  annote = {review membrane protein electrostatic interaction.}
}

@ARTICLE{Hoov86,
  author = {William G. Hoover},
  title = {Constant-pressure equations of motion},
  journal = {Phys. Rev. A},
  year = {1986},
  volume = {34},
  pages = {2499--2500},
  number = {3}
}

@ARTICLE{HOPF86,
  author = {J. J. Hopfield and D. W. Tank},
  title = {Computing with Neural Circuits},
  journal = SCI,
  year = {1986},
  volume = {233},
  pages = {625--633}
}

@INCOLLECTION{HOWA86,
  author = {I. P. Howard},
  title = {The Perception of Posture, Self-motion and the Visual Vertical},
  booktitle = {Handbook of Perception and Human Performance},
  publisher = {John Wiley \& Sons},
  year = {1986},
  editor = {K. R. Boff},
  address = {New York}
}

@ARTICLE{HUAN86,
  author = {H.W. Huang},
  title = {Deformation free energy of bilayer membrane and its effect on gramicidin
	channel lifetime},
  journal = BJ,
  year = {1986},
  volume = {50},
  pages = {1061--1070}
}

@ARTICLE{JONA86B,
  author = {A. Jonas},
  title = {Reconstitution of high-density lipoproteins},
  journal = {Methods Enzymol.},
  year = {1986},
  volume = {128},
  pages = {553}
}

@BOOK{JUNG86A,
  title = {Intellectual Mastery of Nature - Theoretical Physics from {O}hm to
	{E}instein, Vol.~1: The Torch of Mathematics 1800-1870},
  publisher = {Chicago University Press},
  year = {1986},
  author = {C. Jungnickel and R. McCormmach},
  address = {Chicago}
}

@BOOK{JUNG86B,
  title = {Intellectual Mastery of Nature - Theoretical Physics from {O}hm to
	{E}instein, Vol.~2: The Now Mighty Theoretical Physics 1870-1925},
  publisher = {Chicago University Press},
  year = {1986},
  author = {C. Jungnickel and R. McCormmach},
  address = {Chicago}
}

@ARTICLE{KARP86,
  author = {M. Karplus and J. A. McCammon},
  title = {The Dynamics of Proteins},
  journal = {Scientific American},
  year = {1986},
  volume = {4},
  pages = {30}
}

@ARTICLE{KLAP86,
  author = {Isaac Klapper and Ray Hagstrom and Richard Fine and Kim Sharp and
	Barry Honig},
  title = {Focusing of Electric Fields in the Active Site of {Cu-Zn} Superoxide
	Dismutase: Effects of Ionic Strength and Amino-Acid Modification},
  journal = PSFG,
  year = {1986},
  volume = {1},
  pages = {47--59}
}

@ARTICLE{KNAP86,
  author = {E. W. Knapp and P. O. J. Scherer and S. F. Fischer},
  title = {Model studies of low-temperature optical transitions of photochemical
	reaction centers A-, LD-, CD-, ADMR- and LD-ADMR-spectra for {\em
	Rhodopseudomonas viridis}},
  journal = BBA,
  year = {1986},
  volume = {852},
  pages = {295--305}
}

@ARTICLE{KRUS86,
  author = {A.~Krust and S.~Green and P.~Argos and V.~Kumar and P.~Walter and
	J.~Bornert and P.~Chambon},
  title = {The chicken oestrogen receptor sequence: homology with v-{\it erb}{A}
	and the human oestrogen and glucocorticoid receptors.},
  journal = EMBO,
  year = {1986},
  volume = {5},
  pages = {891--897},
  annote = {ref for the domain struct of members of nuclear recp family reference
	also KUMA87}
}

@ARTICLE{KURI86,
  author = {J. Kuriyan and G. A. Petsko and R. M. Levy and M. Karplus},
  title = {Effect of anisotropy and anharmonicity on protein crystallographic
	refinement. {A}n evaluation by molecular dynamics},
  journal = JMB,
  year = {1986},
  volume = {190},
  pages = {227--254},
  annote = {requested Tx=19921104.}
}

@BOOK{Lanc86,
  title = {The Variational Principles of Mechanics},
  publisher = {Dover},
  year = {1986},
  author = {C. Lanczos},
  address = {New York},
  edition = {fourth}
}

@BOOK{LAND86,
  title = {Theory of Elasticity},
  publisher = {Cambridge University Press},
  year = {2005},
  author = {David P. Landau and Kurt Binder},
  edition = {2}
}

@BOOK{LaBi05,
  title = {A Guide to Monte Carlo Simulations in Statistical Physics},
  publisher = {Pergamon Press},
  year = {1986},
  author = {L. D. Landau and E. M. Lifschitz},
  volume = {7},
  series = {Course of theoretical physics},
  address = {Oxford, New York},
  edition = {3}
}

@ARTICLE{LANG86,
  author = {G. Langanger and M. Moeremans and G. Daneels and A. Sobieszek and
	M. {De Brabander} and J. {De Mey}},
  title = {The molecular organisation of myosin in stress fibers of cultured
	cells},
  journal = JCB,
  year = {1986},
  volume = {102},
  pages = {200--209}
}

@ARTICLE{LINS86,
  author = {R. Linsker},
  title = {From Basic Network Principles to Neural Architecture: Emergence of
	Orientation Columns},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1986},
  volume = {83},
  pages = {8779--8783}
}

@ARTICLE{LOHM86,
  author = {T.~M.~Lohman},
  title = {Kinetics of Protein--Nucleic Acid Interactions: Use of Salt Effects
	to Probe Mechanisms of Interaction},
  journal = {CRC Critical Rev.\ Biochem.},
  year = {1986},
  volume = {19},
  pages = {191--245},
  number = {3},
  annote = {lac-repressor {DNA}interaction is based on electrostatics via plots
	of logK(obs) vs. log[MX] where Mx is salt concentraton}
}

@ARTICLE{LUXN86,
  author = {M. Luxnat and H. J. Galla},
  title = {Partition of chlorpromazine into lipid bilayer membranes: {The} effect
	of membrane structure and composition},
  journal = BBA,
  year = {1986},
  volume = {856},
  pages = {274--282},
  annote = {Partition function of chlorpromazine between the aqeous phase and
	lipid bilayer vesicles were dtermined as function of drug concentration,
	lipid chain length, cholestral content and temperature encompassing
	the range of the lipid phase transition. Incorporation of drug does
	not affect membrane structure till 3X10$^{-5}$ M. But the phase-transition
	temparature of lipid membrane is decreased and broadened at high
	drug concentrations. Lipid chain length has some effect on Kd, and
	under phase transition temperature Kd is decreased by at least 10
	times. Cholestral decreases Kd by about 2 times.}
}

@ARTICLE{MADU86,
  author = {J. D. Madura and W. L. Jorgensen},
  title = {Ab initio and {M}onte {C}arlo Calculations for a Nucleophilic addition
	reaction in the Gas Phase and in Aqueous Solution},
  journal = JACS,
  year = {1986},
  volume = {108},
  pages = {2517}
}

@ARTICLE{MAO86,
  author = {S.-Y. Mao and A.H. Maki and G.H. de Haas},
  title = {Optically detected magnetic resonance studies of porcine pancreatic
	phospholipase {A$_2$} binding to a negatively charged substrate analogue},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {2781--2786}
}

@ARTICLE{MCIN86,
  author = {T. J. McIntosh and S. A. Simon},
  title = {Hydration force and bilayer deformation: a reevaluation},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {4058--4066},
  annote = {requested Tx=19920908.}
}

@ARTICLE{MCIN86A,
  author = {T. J. McIntosh and S. A. Simon},
  title = {Area per molecule and distribution of water in fully hydrated dilaurylohsphatidylethanolamine
	bilayers},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {4948--4952},
  annote = {area per lipid of gel and fluid phase DLPE (41.0 to 49.1 {\AA\ }$^2$),
	bilayer thickness (37.2 and 33.0 {\AA\ } between high density peaks.
	Hydration of head group 7 and 9 waters respectively. Very small aqueous
	phase between lamellar (5 {\AA\ }) because of the PE head group.}
}

@BOOK{MILL86,
  title = {Advanced Programming: Design and Structure Using Pascal},
  publisher = {Addison-Wesley},
  year = {1986},
  author = {L. H. Miller}
}

@ARTICLE{MILT86,
  author = {J.~G.~Milton and W.~C.~Galley.},
  title = {Evidence for heterogeneity in {DNA}-associated solvent mobility from
	acridine phosphorescence spectra},
  journal = BP,
  year = {1986},
  volume = {25},
  pages = {1673--1684},
  annote = {shows that water is bound tighter to phosphates than bases at low
	humidities}
}

@ARTICLE{MULL86,
  author = {H. J. M{\"u}ller and M. Luxnat and H. J. Galla},
  title = {Lateral diffusion of small solutes and partition of amphipaths and
	defect structures of lipid bilayers},
  journal = BBA,
  year = {1986},
  volume = {856},
  pages = {283--289},
  annote = {Measured partition coefficient of chlorpromazine into DPPC in fluid,
	gel and ripple phase. Suggest defect (free volumes) are important
	in membrane for absorbing amphipaths.}
}

@ARTICLE{NADL86,
  author = {Walter Nadler and Klaus Schulten},
  title = {Generalized Moment Expansion for Observables of Stochastic Processes
	in Dimensions $d>1$: Application to {M}\"ossbauer Spectra of Proteins},
  journal = JCP,
  year = {1986},
  volume = {84},
  pages = {4015--4025}
}

@ARTICLE{NEUM86,
  author = {M. Neumann},
  title = {Dielectric relaxation in water. Computer simulations with the TIP4P
	potential},
  journal = JCP,
  year = {1986},
  volume = {85},
  pages = {1567--1576}
}

@ARTICLE{HEGE86,
  author = {Dieter Oesterhelt and P. Hegemann and Paul Tavan and Klaus Schulten},
  title = {Trans-Cis Isomerization of Retinal and a Mechanism for Ion Trans\-location
	in Halorhodo\-psin},
  journal = EBJ,
  year = {1986},
  volume = {14},
  pages = {123--129}
}

@ARTICLE{OEST86,
  author = {D.~Oesterhelt and P.~Hegemann and P.~Tavan and K.~Schulten},
  title = {{\it Trans-cis\/} isomerization of retinal and a mechanism for ion
	translocation in halorhodopsin},
  journal = EBJ,
  year = {1986},
  volume = {14},
  pages = {123--129},
  annote = {should be put in tbpub.bib instead}
}

@BOOK{Olve86,
  title = {Applications of Lie Groups to Differential Equations},
  publisher = {Springer-Verlag},
  year = {1986},
  author = {Olver, P.}
}

@ARTICLE{ONUC86,
  author = {Jos{\'e} Nelson Onuchic and David N. Beratan and J. J. Hopfield},
  title = {Some Aspects of Electron-Transfer Reaction Dynamics},
  journal = JPC,
  year = {1986},
  volume = {90},
  pages = {3707--3721}
}

@ARTICLE{PHIL86,
  author = {J. B. Phillips},
  title = {Two Magnetoreception Pathways in a Migratory Salamander},
  journal = SCI,
  year = {1986},
  volume = {233},
  pages = {765--767}
}

@ARTICLE{POLL86,
  author = {H. Polland and M. A. Franz and W. Zinth and W. Kaiser and E. K{\"o}lling
	and D. Oesterhelt},
  title = {Early Picosecond Events in the Photocycle of Bacteriorhodopsin},
  journal = BJ,
  year = {1986},
  volume = {49},
  pages = {651--662}
}

@ARTICLE{RaSc86,
  author = {A. Rahman and J.~P. Schiffer},
  title = {Structure of a One-Component Plasma in an External Field: A Molecular-Dynamics
	Study of Particle Arrangement in a Heavy-Ion Storage Ring},
  journal = PRL,
  year = {1986},
  volume = {57},
  pages = {1133--1136},
  number = {9}
}

@ARTICLE{RIEG86,
  author = {J. Riegler and H. M{\"o}hwald},
  title = {Elastic interactions of photosynthetic reaction center proteins affecting
	phase transitions and protein distributions},
  journal = BJ,
  year = {1986},
  volume = {49},
  pages = {1111--1118}
}

@ARTICLE{RITT86,
  author = {Helge Ritter and Klaus Schulten},
  title = {On the Stationary State of {K}ohonen's Self-Organizing Sensory Mapping},
  journal = BC,
  year = {1986},
  volume = {54},
  pages = {99--106}
}

@INPROCEEDINGS{RITT86A,
  author = {Helge Ritter and Klaus Schulten},
  title = {Topology Conserving Mappings for Learning Motor Tasks},
  booktitle = {Neural Networks for Computing},
  year = {1986},
  editor = {J. S. Denker},
  pages = {376--380},
  publisher = {American Institute of Physics Publication, Conference Proceedings
	151},
  annote = {This conference took place in Snowbird, Utah.}
}

@ARTICLE{SAND86,
  author = {D. Sandorfy and D. Vocelle},
  title = {The photochemical event in rhodopsins},
  journal = {Can. J. Chem.},
  year = {1986},
  volume = {64},
  pages = {2251--2266}
}

@INCOLLECTION{SaVa86,
  author = {J. M. Sanz-Serna and F. Vadillo},
  title = {Nonlinear Instability, the Dynamic Approach},
  booktitle = {Numerical Analysis},
  publisher = {Pitman Research Notes in Math. 140},
  year = {1986},
  editor = {D. F. Griffiths and G. A. Watson},
  pages = {187--199},
  address = {Longman Scientific and Technical, London}
}

@ARTICLE{SCHR86A,
  author = {J.~Schreiber and T.E.~Eling and R.P.~Mason},
  title = {{The oxidation of arachidonic acid by the cyclooxygenase activity
	of purified prostaglandin H synthase: spin trapping of a carbon-centered
	free radical intermediate.}},
  journal = {Arch.\ Biochem.\ Biophys.},
  year = {1986},
  volume = {249},
  pages = {126--136},
  number = {1}
}

@ARTICLE{SCHU86B,
  author = {Klaus Schulten},
  title = {Continuous Fluorescence Microphotolysis by a $\sin^2 kx$ Grating},
  journal = CPL,
  year = {1986},
  volume = {124},
  pages = {230--236}
}

@INCOLLECTION{SCHU86C,
  author = {Klaus Schulten},
  title = {Magnetic Field Effects on Radical Pair Processes in Chemistry and
	Biology},
  booktitle = {Biological Effects of Static and Extremely Low Frequency Magnetic
	Fields},
  publisher = {{MMV Medizin Verlag}},
  year = {1986},
  editor = {J. H. Bernhard},
  pages = {133--140},
  address = {Munich}
}

@ARTICLE{SCHU86A,
  author = {Klaus Schulten and Robert Bittl},
  title = {Probing the Dynamics of a Polymer with Paramagnetic End Groups by
	Magnetic Fields},
  journal = JCP,
  year = {1986},
  volume = {84},
  pages = {5155--5161}
}

@INCOLLECTION{SCHU86D,
  author = {Klaus Schulten and Andreas Windemuth},
  title = {Model for a Physiological Magnetic Compass},
  booktitle = {Biophysical Effects of Steady Magnetic Fields},
  publisher = {Springer},
  year = {1986},
  editor = {G. Maret and N. Boccara and J. Kiepenheuer},
  volume = {11},
  series = {Proceedings in Physics},
  pages = {99--106},
  address = {Berlin}
}

@ARTICLE{SCHU86,
  author = {Zan Schulten and Klaus Schulten},
  title = {Proton Conduction through Proteins: An Overview of Theoretical Principles
	and Applications},
  journal = ME,
  year = {1986},
  volume = {127},
  pages = {419--438}
}

@ARTICLE{SCOT86,
  author = {H.L. Scott},
  title = {{M}onte {C}arlo calculations of oder parameter profiles in models
	of lipid--protein interactions in bilayers},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {6122--6126}
}

@ARTICLE{SELD85,
  author = {Lynn A. Selden and Lewis C. Gershman and James E. Estes},
  title = {A kinetic comparison between {Mg}-actin and {Ca}-actin},
  journal = JMRCM,
  year = {1986},
  volume = {7},
  pages = {215--224}
}

@ARTICLE{SEMM86,
  author = {P. Semm and C. Demaine},
  title = {Neurophysiological properties of magnetic cells in the pigeon's visual
	system},
  journal = {J.~Comp.~Physiol.~A},
  year = {1986},
  volume = {159},
  pages = {619--625}
}

@ARTICLE{SHEV86,
  author = {M. Sheves and A. Albeck and N. Friedman and M. Ottolenghi},
  title = {Controlling the {pK}$_{{\rm a}}$ of the Bacteriorhodopsin {Schiff}-Base
	by Use of Artificial Retinal Analogs},
  journal = PNAS,
  year = {1986},
  volume = {83},
  pages = {3262--3266}
}

@ARTICLE{SHUE86,
  author = {D.~J.~Shuey and C.~S.~Parker},
  title = {Bending of promoter {\sc DNA} on binding of heat shock transcription
	factor.},
  journal = NAT,
  year = {1986},
  volume = {323},
  pages = {459--461},
  annote = {eukaryotic system, bends DNA, not read}
}

@ARTICLE{SING86,
  author = {U. C. Singh and P. A. Kollman},
  title = {A combined ab initio quantum mechanical and molecular mechanical
	method for carrying out simulations on complex molecular systems:
	applications to the {CH}$_3$/{Cl+Cl$^-$} exchange reaction and gas
	phase protonation},
  journal = JCC,
  year = {1986},
  volume = {7},
  pages = {718}
}

@BOOK{SMAL86,
  title = {The Physical Chemistry of Lipids},
  publisher = {Plenum Publishing Corp.},
  year = {1986},
  author = {Donald M. Small},
  number = {4},
  pages = {672},
  series = {Handbook of Lipid Research},
  address = {New York},
  annote = {very good book with MANY details on lipids, but not so much on membranes;
	explains what the different states (crystal, gel, liquid crystal,
	fluid) are; many data; main phase transition temperature for POPC
	in excess water -5C...+4C; angle of tilt determined by the kind of
	headgroup (p.478); PC is amphiphilic in water (p.481); gel->LC is
	a chain melting transition (p.485); DPPC: crystalline state has chains
	parallel to bilayer normal, in gel (L_\beta') state chains are tilted,
	in the ripple phase (P_\beta') surface ondulations occur (period:
	160\AA...140\AA) and the chains are parallel again, in the LC (L_\alpha)
	phase (sometimes referred to as the fluid phase) the chains are melted
	(trans->cis) and tilt and ripples are gone again (p487)},
  keywords = {cholesterol; lipid; membrane; POPC (p.507); DPPC},
  suggestions = {look at headgroup angle P--N vector: 17deg. and 27deg. (p138); look
	at hydrogen bonding network (p.138); interdigitation; look at tilt
	angle of lipid chain vs. bilayer normal: this also helps to identify
	the phase (p.486f)}
}

@ARTICLE{SMIT85,
  author = {Jeremy Smith and Stephen Cusack and Ulrik Pezzeca and Bernard Brooks
	and Martin Karplus},
  title = {Inelastic Neutron Scattering Analysis of Low Frequency in Proteins:
	A Normal Mode Study of the Bovine Pancreatic Trypsin Inhibitor},
  journal = JCP,
  year = {1986},
  volume = {85},
  pages = {3636--3654}
}

@ARTICLE{SMIT86,
  author = {S. O. Smith and I. Hornung and R. {van der Steen} and J. A. Pardoen
	and M. S Braiman and J. Lugtenburg and R. A. Mathies},
  title = {Are {C$_{14}$}-{C$_{15}$} Single Bond Isomerizations of the Retinal
	Chromophore Involved in the Proton-Pumping Mechanism of Bacteriorhodopsin?},
  journal = PNAS,
  year = {1986},
  volume = {83},
  pages = {967--971}
}

@ARTICLE{SMITH96,
  author = {S. O. Smith and I. Hornung and van der Steen, R and J. A. Pardoen
	and M. S. Braiman and J. Lugtenburg and R. Mathies},
  title = {Are C$_14$-C$_15$ single bond isomerizations of the retinal chromophore
	involved in the proton-pumping mechanism of bacteriorhodopsin?},
  journal = PNAS,
  year = {1986},
  volume = {83},
  pages = {967--971}
}

@BOOK{StWe86,
  title = {Lie Groups and Algebras with Applications to Physics, Geometry, and
	Mec hanics},
  publisher = {Springer-Verlag},
  year = {1986},
  author = {D. H. Stattinger and O. L. Weaver},
  address = {Berlin}
}

@ARTICLE{STRA86,
  author = {T. P. Straatsma and H. J. C. Berendsen and A. J. Stam},
  title = {Estimation of statistical errors in molecular simulation calculations},
  journal = MP,
  year = {1986},
  volume = {57},
  pages = {89--95},
  number = {1},
  annote = {they give a method to determine the statistical error of a mean (like
	kinetic energy) by means of variance/covariance calculations without
	having to know the correlations}
}

@ARTICLE{SUMI86,
  author = {H. Sumi and R. A. Marcus},
  title = {Dynamical Effects in Electron Transfer Reactions},
  journal = JCP,
  year = {1986},
  volume = {84},
  pages = {4894--4914}
}

@ARTICLE{SWEE86,
  author = {Robert M. Sweet},
  title = {Evolutionary Similarity Among Peptide Segments Is a Basis for Prediction
	of Protein Folding},
  journal = BP,
  year = {1986},
  volume = {25},
  pages = {1565}
}

@ARTICLE{TAVA86,
  author = {Paul Tavan and Klaus Schulten},
  title = {Evidence for a 13,14-cis Cycle in Bacteriorhodopsin},
  journal = BJ,
  year = {1986},
  volume = {50},
  pages = {81--89}
}

@ARTICLE{TAVA86A,
  author = {Paul Tavan and Klaus Schulten},
  title = {The Low-Lying Electronic Excitations in Long Polyenes: {A} {PPP--MRD--CI}
	Study},
  journal = JCP,
  year = {1986},
  volume = {85},
  pages = {6602--6609},
  number = {11},
  annote = {DEC 1}
}

@ARTICLE{TREU86,
  author = {Herbert Treutlein and Klaus Schulten},
  title = {Noise-Induced Neural Impulses},
  journal = EBJ,
  year = {1986},
  volume = {13},
  pages = {355--365}
}

@ARTICLE{TOTH86,
  author = {R. {T{\'o}th-Bocon{\'a}di} and S. G. Hristova and L. Keszthelyi},
  title = {Diamines Reverse the Direction on the Bacteriorhodopsin Proton Pump},
  journal = FEBS,
  year = {1986},
  volume = {195},
  pages = {164--168}
}

@ARTICLE{VADA86,
  author = {P. Vadas and W. Pruzanski},
  title = {Role of secretory phospholipase {A$_2$} in the pathobiology of disease},
  journal = {Lab. Invest.},
  year = {1986},
  volume = {55},
  pages = {391--398},
  annote = {Pharmaceutical aspecst of PLA2, get it.}
}

@ARTICLE{VOLW86,
  author = {J.J. Volwerk and P.C. Post and G.H. de Haas and O. H. Griffith},
  title = {Activation of Porcine Pancreatic Phospholipase {A$_2$} by the presence
	of negative charges at the lipid--water interface},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {1726--1733},
  annote = {preference for negatively charged lipids}
}

@ARTICLE{HIPP86,
  author = {P. H. {Von Hippel} and O. G. Berg},
  title = {On the specificity of {DNA}-protein interactions},
  journal = PNAS,
  year = {1986},
  volume = {83},
  pages = {1608--1612}
}

@BOOK{WUTH86,
  title = {{NMR} of proteins and nuclear acids},
  publisher = {Wiley-Interscience},
  year = {1986},
  author = {K. W\"utrich},
  address = {New York}
}

@ARTICLE{WALT86,
  author = {A. Walter and J. Gutknecht},
  title = {Permeability of small nonelectrolytes through lipid bilayer membranes},
  journal = {J. Membrane Biol.},
  year = {1986},
  volume = {90},
  pages = {207--217},
  annote = {Permeability of 22 solutes compared to their partition coefficient
	in hexane, olive oil, octanol and ether. They find correlation is
	better for nonpolar solvents. The effect of volume is inversely correlated
	to the permeability, but for small molecules such a relation is steep
	and can not explained by Stokes-Einstein model of diffusion. They
	suggest membrane behave more like polymer than liquid hydrocarbon.
	Also, they suggest for the molecules tested the permeability is mainly
	controlled by the diffusion process in membrane itself. }
}

@ARTICLE{WARS86,
  author = {Arieh Warshel and Jenn-Kang Hwang},
  title = {Simulations of the Dynamics of Electron Transfer Reactions in Polar
	Solvent: Semiclassical Trajectories and Dispersed Polaron Approaches},
  journal = JCP,
  year = {1986},
  volume = {84},
  pages = {4938--4957}
}

@ARTICLE{WASI86,
  author = {M. R. Wasielewski and P. A. Liddell and D. Barrett and T. A. Moore
	and D. Gust},
  title = {Ultrafast carotenoid to pheophorbide energy transfer in a biomimetic
	model for antenna function in photosynthesis},
  journal = NAT,
  year = {1986},
  volume = {322},
  pages = {570--572}
}

@ARTICLE{WONG86,
  author = {C. F. Wong and J. A. McCammon},
  title = {Computer Simulation and the Design of New Biological Molecules},
  journal = {Isr\ J.\ Chem.},
  year = {1986},
  volume = {27},
  pages = {211--215}
}

@ARTICLE{ZING86,
  author = {Jesmael Zingoni and Yat Sun Or and Rosalie K. Crouch and Chung-Ho
	Chang and Rajni Govindjee and Thomas G. Ebrey},
  title = {Effect of Variation of Retinal Polyene Side-Chain Length on Formation
	and Function of Bacteriorhodopsin Analogue Pigments},
  journal = BCH,
  year = {1986},
  volume = {25},
  pages = {2022--2027}
}

@INCOLLECTION{Aars85,
  author = {Sverre J. Aarseth},
  title = {Direct Methods for {N}-Body Simulations},
  booktitle = {Multiple Time Scales},
  publisher = {Academic Press, Inc.},
  year = {1985},
  editor = {Jeremiah U. Brackill and Bruce I. Cohen},
  chapter = {12},
  pages = {377--418},
  annote = {4th order polynomial; overview article},
  isbn = {0-12-123420-7},
  keywords = {gravitation; astrophysics; distance classes; multiple time steps;
	adaptive time steps; integration scheme; relative accuracy; individual
	time steps; algorithm}
}

@ARTICLE{Aizu85,
  author = {K. Aizu},
  title = {Canonical Transformation Invariance and Linear Multistep Formula
	for Integration of \mbox{Hamiltonian} Systems},
  journal = {J. Comput. Phys.},
  year = {1985},
  volume = {58},
  pages = {270--274}
}

@ARTICLE{AlMc85,
  author = {Allison, S. A. and McCammon, J. A.},
  title = {Dynamics of Substrate Binding to Copper Zinc Superoxide Dismutase},
  journal = {J. Phys.\ Chem.},
  year = {1985},
  volume = {89},
  pages = {1072}
}

@ARTICLE{Appe85,
  author = {A. W. Appel},
  title = {An Efficient Program for Many-Body Simulation},
  journal = SJSSC,
  year = {1985},
  volume = {6},
  pages = {85--103}
}

@INPROCEEDINGS{BevG85,
  author = {H.~J.~C. Berendsen and W.~F. van Gunsteren},
  title = {Practical Algorithms for Dynamic Simulations},
  booktitle = {Molecular Dynamics Simulations of Statistical Mechanical Systems,
	Proceedings of the Enrico Fermi Summer School, Verenna},
  year = {1985},
  editor = {G. Ciccoti and W. G. Hoover},
  pages = {43--65},
  organization = {Soc. Italiana di Fisica, Bologne}
}

@INCOLLECTION{BITT85,
  author = {Robert Bittl and Herbert Treutlein and Klaus Schulten},
  title = {Electron Conduction along Aliphatic Chains},
  booktitle = {Antennas and Reaction Centers of Photosynthetic Bacteria --- {S}tructure,
	Interaction and Dynamics},
  publisher = {Springer},
  year = {1985},
  editor = {M. Michel-Beyer\-le},
  pages = {264--276}
}

@ARTICLE{BRAD85,
  author = {S.T. Brady},
  title = {A novel brain {ATP}ase with properties expected for the fast axonal
	transport motor},
  journal = NAT,
  year = {1985},
  volume = {317},
  pages = {73--75}
}

@ARTICLE{BROO85A,
  author = {Charles L. {Brooks~I{}I{}I} and B. Montgomery Pettitt and Martin
	Karplus},
  title = {Structural and energetic effects of truncating long range interactions
	in ionic and polar fluids},
  journal = JCP,
  year = {1985},
  volume = {83},
  pages = {5897--5908},
  number = {11},
  annote = {also mentions effects from finite system size (boundary effects);
	uses integral equations instead of simulations; truncation causes
	large effects, e.g. in distribution functions},
  keywords = {spherical truncation; Ornstein-Zernik integral equation; TIPS water
	model}
}

@ARTICLE{BROO85,
  author = {C. L. {Brooks~{III}} and A. Br{\"u}nger and M. Karplus},
  title = {Active Site Dynamics in Protein Molecules: A Stochastic Boundary
	Molecular-Dynamics Approach},
  journal = BP,
  year = {1985},
  volume = {24},
  pages = {843}
}

@ARTICLE{BRUN85,
  author = {Axel Br{\"u}nger and Reiner Peters and Klaus Schulten},
  title = {Continuous Fluorescence Microphotolysis to Observe Lateral Diffusion
	in Membranes: Theoretical Methods and Applications},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {2147--2160}
}

@ARTICLE{BUHM85,
  author = {Joachim Buhmann and Helge Ritter and Klaus Schulten},
  title = {Neuro-Kyber\-netik und k\"unstliche {I}ntelligenz},
  journal = CW,
  year = {1985},
  volume = {25}
}

@ARTICLE{BURG85,
  author = {R.~W.~Burlingame and W.~E.~Love and B.-C.~Wang and R.~Hamlin and
	N.-H.~Xuong and E.~N.~Moudrianakis},
  title = {Crystallographic structure of the octameric histone core of the nucleosome
	at a resolution of {3.3\,\AA}},
  journal = SCI,
  year = {1985},
  volume = {228},
  pages = {546--553}
}

@INCOLLECTION{CARS85,
  author = {M. Carson and J. Hermans},
  title = {The Molecular Dynamics Workshop Laboratory},
  booktitle = {Molecular Dynamics and Protein Structure},
  publisher = {University of North Carolina},
  year = {1985},
  editor = {J. Hermans},
  pages = {165--166},
  address = {Chapel Hill}
}

@ARTICLE{CEVC85,
  author = {G. Cevc and Derek Marsh},
  title = {Hydration of noncharged lipid bilayer membranes. Theory and experiments
	with phosphatidylethanolamines},
  journal = BJ,
  year = {1985},
  volume = {47},
  pages = {21--31},
  annote = {hydration theory and measured free energy of PE membranes}
}

@ARTICLE{CHAN85A,
  author = {J. Chandrasekhar and S. F. Smith and W. L. Jorgensen},
  title = {Theoretical Examination of the SN2 Reaction involving Chloride Ion
	and Methyl Chloride in the Gas Phase and Aqueous Solution},
  journal = JACS,
  year = {1985},
  volume = {107},
  pages = {154}
}

@ARTICLE{Chaw85,
  author = {M. M. Chawla},
  title = {On the order and attainable intervals of periodicity of explicit
	{N}ystr{\"o}m methods for $y''=f(t,y)$},
  journal = SJNA,
  year = {1985},
  volume = {22},
  pages = {127--131}
}

@INPROCEEDINGS{CROF85,
  author = {Antony R. Crofts},
  title = {The mechanism of ubiquinol:cytochrome c oxidoreductases of mitochondria
	and of {\em Rhodopseudomonas sphaeroides}},
  booktitle = {The Enzymes of Biological Membranes},
  year = {1985},
  editor = {A. N. Martonosi},
  volume = {4},
  pages = {347--382},
  publisher = {Plenum, New York},
  annote = {modified Q-cycle}
}

@ARTICLE{CURY85,
  author = {B. Curry and I. Palings and A. Broek and J. Pardoen and J. Lugtenburg
	and R. Mathies},
  title = {Vibrational Analysis of the Retinal Isomers},
  journal = AIRS,
  year = {1985},
  volume = {12},
  pages = {115--178}
}

@ARTICLE{DEIS85,
  author = {J. Deisenhofer and O. Epp and K. Mikki and R. Huber and H. Michel},
  title = {Structure of the protein subunits in the photosynthetic reaction
	centre of {{\em Rhodopseudomonas viridis}} at 3 {{\AA}} resolution},
  journal = NAT,
  year = {1985},
  volume = {318},
  pages = {618--624},
  annote = {requested Tx=19921018.}
}

@ARTICLE{DRAT85,
  author = {E. Dratz and J. Van Breemen and K. Paul Kamps and W. Keegstra and
	E. Van Bruggen},
  title = {Two-dimentional Crystallization of Bovine Rhodopsin},
  journal = BBA,
  year = {1985},
  volume = {832},
  pages = {337--342}
}

@ARTICLE{EISE85,
  author = {E. Eisenberg and T. L. Hill},
  title = {Muscle contraction and free energy transduction in biological systems},
  journal = SCI,
  year = {1985},
  volume = {227},
  pages = {999}
}

@INPROCEEDINGS{Feng85,
  author = {K. Feng},
  title = {On Difference Schemes and Symplectic Geometry},
  booktitle = {Proc. 1984 Beijing Symposium on Differential Geometry and Differential
	Equations{\rm ---}Computation of Differential Equations},
  year = {1985},
  editor = {K. Feng},
  pages = {42--58},
  address = {Science Press, Beijing}
}

@BOOK{FERS85,
  title = {Enzyme structure and mechanism},
  publisher = {W.H. Freeman and Co.},
  year = {1985},
  author = {A. Fersht},
  address = {New York}
}

@ARTICLE{FRIE85,
  author = {Friesner, R. A.},
  title = {Solution of Self-Consistent Field Electronic Structure Equations
	by a Pseudospectral Method},
  journal = CPL,
  year = {1985},
  volume = {116},
  pages = {39}
}

@BOOK{GARD85,
  title = {Handbook of Stochastic Methods for Physics, Chemistry, and the Natural
	Sciences},
  publisher = {Springer-Verlag},
  year = {1985},
  author = {C. W. Gardiner},
  address = {New York}
}

@ARTICLE{GARG85,
  author = {Anupam Garg and Jos{\'e} Nelson Onuchic and Vinay Ambegaokar},
  title = {Effect of Friction on Electron Transfer in Biomolecules},
  journal = JCP,
  year = {1985},
  volume = {83},
  pages = {4491--4503}
}

@ARTICLE{GILS85,
  author = {Michael K.\ Gilson and Alexander Rashin and Richard Fine and Barry
	Honig},
  title = {On the Calculation of Electrostatic Interactions in Proteins},
  journal = JMB,
  year = {1985},
  volume = {183},
  pages = {503--516}
}

@ARTICLE{GREE85,
  author = {R. E. Greenblatt and Y. Blatt and M. Montal},
  title = {The structure of the voltage-sensitive sodium channel},
  journal = FEBS,
  year = {1985},
  volume = {193},
  pages = {125--134}
}

@ARTICLE{HARB85,
  author = {G. S. Harbison and S. O. Smith and J. A. Pardoen and J. M. L. Courtin
	and J. Lugtenburg and J. Herzfeld and R. A. Mathies and R. G. Griffin},
  title = {Solid-State $^{13}${C} {NMR} Detection of a Perturbed 6-s-{\it trans\/}
	Chromophore in Bacteriorhodopsin},
  journal = BCH,
  year = {1985},
  volume = {24},
  pages = {6955--6962}
}

@ARTICLE{HOGL85,
  author = {J.~M.~Hogle and M.~Chow and D.~J.~Filman},
  title = {Three-dimensional Structure of Poliovirus at {2.9\,{\AA} }Resolution},
  journal = SCI,
  year = {1985},
  volume = {229},
  pages = {1358}
}

@ARTICLE{Hoov85,
  author = {William G. Hoover},
  title = {Canonical dynamics: Equilibrium phase-space distribution},
  journal = {Phys. Rev. A},
  year = {1985},
  volume = {31},
  pages = {1695--1697},
  number = {3}
}

@ARTICLE{HOPF85,
  author = {J. J. Hopfield and D. W. Tank},
  title = {``Neural'' Computation of Decisions in Optimization Problems},
  journal = {Biological Cybernetics},
  year = {1985},
  volume = {52},
  pages = {141--152}
}

@ARTICLE{KAJI85,
  author = {S. Kaji and N. Kawabata},
  title = {Neural Interactions of two Moving Patterns in the Direction and Orientation
	Domain in the Complex Cells of Cat's Visual Cortex},
  journal = {Vis. Res.},
  year = {1985},
  volume = {25},
  pages = {749--753}
}

@ARTICLE{KAO85,
  author = {Shih-Chung Kao and Elisabeth V. Bobst and Gary T. Pauly and Albert
	M. Bobst},
  title = {Molecular Dynamics in Protein-Single Stranded {DNA} complexes. Two
	Distinct Mobilities in Pol(deoxythymidylic acid)-Gene 5 Protein Complexes},
  journal = JBSD,
  year = {1985},
  volume = {3},
  pages = {261--268}
}

@ARTICLE{KIRS85A,
  author = {J.L. Kirschvink and M.M. Walker and S.B. Chang and A.E. Dizon and
	K.A. Peterson},
  title = {Chains of single-domain magnetite particles in chinook salmon, {\em
	{O}ncorhynchus tschawytscha}},
  journal = {J.~Comp.~Physiol.~A},
  year = {1985},
  volume = {157},
  pages = {375--381}
}

@BOOK{KIRS85,
  title = {Magnetic biomineralization and magnetoreception in organisms},
  publisher = {Plenum},
  year = {1985},
  author = {J.~L.~Kirschvink and D.S. Jones and B.L. MacFadden},
  address = {New York}
}

@ARTICLE{KJEL85,
  author = {R. Kjellander and S. Mar\v{c}elja},
  title = {Polarization of water between molecular surfaces: a molecular dynamics
	study},
  journal = CS,
  year = {1985},
  volume = {25},
  pages = {73--80},
  annote = {requested Tx=19921108.}
}

@ARTICLE{KNOW85,
  author = {P.\ J.\ Knowles and H-J.\ Werner},
  title = {An Efficient Second-Order {MC} {SCF} Method for Long Configuration
	Expansions},
  journal = CPL,
  year = {1985},
  volume = {115},
  pages = {259--267}
}

@ARTICLE{KNOW85X,
  author = {P.~J. Knowles and H.-J. Werner},
  title = {{An Efficient Second-Order MC SCF Method for Long Configuration Expansions}},
  journal = CPL,
  year = {1985},
  volume = {115},
  pages = {259--267}
}

@ARTICLE{KYGP85,
  author = {M. L. Kopka and C. Yoon and D. Goodsell and P. Pjura and R. E. Dickerson},
  title = {Binding of an antidrug to {DNA}, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G},
  journal = {J. Mol. Biol.},
  year = {1985},
  volume = {183},
  pages = {553--63},
  number = {4}
}

@ARTICLE{LATT85,
  author = {E. Lattman},
  title = {Diffraction methods for biological macromolecules. {U}se of the rotation
	and translation functions.},
  journal = {Methods in Enzymology},
  year = {1985},
  volume = {115},
  pages = {55}
}

@ARTICLE{LEGG87,
  author = {A. J. Leggett and S. Chakravarty and A. T. Dorsey and Matthew P.
	A. Fisher and Anupam Garg and W. Zwerger},
  title = {Dynamics of the Dissipative Two-State System},
  journal = RMP,
  year = {1985},
  volume = {59},
  pages = {1--85}
}

@ARTICLE{LEVI85,
  author = {M. Levitt and C. Sander and P. S. Stern},
  title = {Protein Normal-Mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease
	and Lysozyme},
  journal = {J.\ Mol.\ Biol.},
  year = {1985},
  volume = {181},
  pages = {423--447}
}

@ARTICLE{LUED85,
  author = {K. M. L{\"u}deke and P. R{\"o}schmann and R. Tischler},
  title = {Suscepitibility Artifacts in NMR Imaging},
  journal = {Magnetic Resonance Imaging},
  year = {1985},
  volume = {3},
  pages = {329--343},
  brief = {Quoted in nih proposal}
}

@ARTICLE{MARC85,
  author = {R. A. Marcus and N. Sutin},
  title = {Electron transfers in chemistry and biology},
  journal = BBA,
  year = {1985},
  volume = {811},
  pages = {265--322}
}

@ARTICLE{NADL85,
  author = {Walter Nadler and Klaus Schulten},
  title = {Generalized Moment Expansion for {B}rownian Relaxation Processes},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {151--160}
}

@ARTICLE{NADL85B,
  author = {Walter Nadler and Klaus Schulten},
  title = {Mean Relaxation Time Approximation for Dynamical Correlation Functions
	in Stochastic Systems near Instabilities},
  journal = ZPB,
  year = {1985},
  volume = {59},
  pages = {53--61}
}

@ARTICLE{NADL85A,
  author = {Walter Nadler and Paul Tavan and Klaus Schulten},
  title = {A Model for the Lateral Diffusion of `Stiff' Chains in a Lipid Bilayer},
  journal = EBJ,
  year = {1985},
  volume = {12},
  pages = {25--31},
  annote = {very theoretical, more on thermodynamics than bilayers},
  keywords = {lipid diffusion; random walk; multistate random walk; master equations;
	2 dimensions}
}

@ARTICLE{NEUM85,
  author = {M. Neumann},
  title = {The dielectric constant of water. {C}omputer simulations with the
	{MCY} model},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {5663--5676}
}

@ARTICLE{NEWT85,
  author = {D.L Newton and C.B. Klee and J. Woodgett and P. Cohen},
  title = {Selective Effects of {CAPP1}-Calmodulin on its Target Proteins},
  journal = BBA,
  year = {1985},
  volume = {845},
  pages = {533--539}
}

@ARTICLE{NORT85,
  author = {Scott H. Northrup and Marc S. Curvin},
  title = {Molecular Dynamics Simulation of Disorder Transitions in Lipid Monolayers},
  journal = JPC,
  year = {1985},
  volume = {89},
  pages = {4707--4713},
  annote = {78ps MD simulation; isolated gauche almost as likely as kinks; good
	general introductory remarks; periodic boundaries; headgroups restrained
	with 800kcal/(mol A^2) which is realized to be bad; observed two
	kinks without biased potential, did not observe crankshaft motion},
  keywords = {membrane; free energy; umbrella sampling; kink transitions; chain
	tilting; disorder phase transition; gateing process},
  suggestions = {surface roughness from movement of headgroups in and out of the solvent;
	study kink disorder; is there crankshaft motion?}
}

@ARTICLE{OELZ85,
  author = {J. Oelze},
  title = {Analysis of bacteriochlorophylls},
  journal = {Methods Microbiol.},
  year = {1985},
  volume = {18},
  pages = {257}
}

@INCOLLECTION{OSTL85,
  author = {N. S. Ostlund and R. A. Whiteside},
  title = {A machine architecture for molecular dynamics: the systolic loop},
  booktitle = {Macromolecular Structure and Specificity: Computer-Assisted Modeling
	and Applications},
  publisher = {Annals of the NY Acad. of Sciences 439},
  year = {1985},
  editor = {B. Venkataraghavan and R. J. Feldman},
  pages = {195--208},
  address = {New York}
}

@INCOLLECTION{OsWh85,
  author = {N. S. Ostlund and R. A. Whiteside},
  title = {A Machine Architecture for Molecular Dynamics: the Systolic Loop},
  booktitle = {Macromolecular Structure and Specifying: Computer-Assisted Modeling
	and Applications},
  publisher = {Annals of the N. Y. Acad of Sciences 439},
  year = {1985},
  editor = {B. Venkataraghavan and R. J. Feldman},
  pages = {195--208},
  address = {New York}
}

@ARTICLE{RENA85,
  author = {M. Renard and M. Delmelle},
  title = {{pH} and Salt Effects on the Slow Intermediates of the Bacteriorhodopsin
	Photocycle\ --\ A Flash-Photolysis Study},
  journal = EBJ,
  year = {1985},
  volume = {12},
  pages = {223--228}
}

@ARTICLE{RENE85,
  author = {R. Renetseder and S. Brunie and B. W. Dijkstra and J. Drenth and
	P. B. Sigler},
  title = {A Comparison of the Crystal Structures of Phospholipase~{A}$_2$ From
	Bovine Pancreas and Crotalus Atrox Venom},
  journal = JBC,
  year = {1985},
  volume = {260},
  pages = {11627--11634}
}

@ARTICLE{RICH85,
  author = {Richardson, J. S.},
  title = {Describing patterns of protein tertiary structure},
  journal = {Methods in Enzymology},
  year = {1985},
  volume = {115},
  pages = {341--380}
}

@ARTICLE{RUSS85,
  author = {S.\ T.\ Russell and A. Warshel},
  title = {Calculations of Electrostatic Energies in Proteins},
  journal = JMB,
  year = {1985},
  volume = {185},
  pages = {389--404}
}

@ARTICLE{SCHA85,
  author = {G. J. M. van Scharrenburg and A. J. Slotboom and G. H. de Haas and
	P. Mulqueen and P. J. Breen and W. D. {Horrocks, Jr.}},
  title = {Catalytic {Ca$^{2+}$} binding site of pancreatic phospholipase {A}$_2$:
	Laser-Induced {Eu}$^{3+}$ Luminescene Study},
  journal = BCH,
  year = {1985},
  volume = {24},
  pages = {334--339},
  annote = {{Eu}$^{3+}$ Luminescene study of water bound in {Ca} binding site.
	Dehydration of {Ca} binding site in micelle-{PLA2} complex}
}

@ARTICLE{SCHI85,
  author = {R. Schiffmiller and R. H. Callender and W. H. Waddell and R. Govindgiee
	and T. G. Ebrey and H. Kakitani and B. Honig and K. Nakanishi},
  title = {Resonance Raman Studies of Bacteriorhodopsin Analogues},
  journal = PCPB,
  year = {1985},
  volume = {41},
  pages = {563--567}
}

@ARTICLE{SCHO85,
  author = {M. Scholz and Klaus Schulten and Reiner Peters},
  title = {Single-Cell Flux Measurement by Continuous Fluorescence Microphotolysis},
  journal = EBJ,
  year = {1985},
  volume = {13},
  pages = {37--44}
}

@ARTICLE{SCHU85B,
  author = {Klaus Schulten},
  title = {The Effect of Intramolecular Paramagnetic--Diamagnetic Ex\-change
	on the Magnetic Field Effect of Radical Pair Recombination},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {1312--1316}
}

@ARTICLE{SCHU85,
  author = {Zan Schulten and Klaus Schulten},
  title = {Model for the Resistance of the Proton Channel Formed by the Proteolipid
	of {ATP}ase},
  journal = EBJ,
  year = {1985},
  volume = {11},
  pages = {149--155}
}

@ARTICLE{SEBB85,
  author = {P. Sebban and B. Robert and G. Jolchine},
  title = {Isolation and Spectroscopic Characterization of the B875 Antenna
	Complex of a Mutant of {\em Rhodopseudomonas sphaeroides}},
  journal = PCPB,
  year = {1985},
  volume = {42},
  pages = {573--578},
  number = {5}
}

@ARTICLE{SEIB85,
  author = {G.~L.~Seibel and U.~C.~Singh and P.~A.~Kollman},
  title = {A molecular dynamics simulation of double-helical {B-DNA} including
	counterions and water},
  journal = PNAS,
  year = {1985},
  volume = {82},
  pages = {6537--6540},
  annote = {counterions on {DNA}and full charge groups positive hexhydrated ions,
	plots of glycosidic angle vs. sugar pucker, NA 3\AA along o-p-o,
	equilibrated TIP3 replicated to cover upto 9\AA solvation shell,
	106\ps, 10\AA cut-off, 2fs timestep, no periodic boundaries, good
	paper!!}
}

@ARTICLE{SEIT85,
  author = {Charles L. Seitz},
  title = {The Cosmic Cube},
  journal = CACM,
  year = {1985},
  volume = {28},
  pages = {22--33},
  number = {1}
}

@ARTICLE{SHAR85,
  author = {A. V. Sharkov and A. V. Pakulev and S. V. Chekalin and Y. A. Matveetz},
  title = {Primary Events in Bacteriorhodopsin},
  journal = BBA,
  year = {1985},
  volume = {808},
  pages = {94--102}
}

@BOOK{SILV85,
  title = {The Physical Chemistry of Membranes: an Introduction to the Structure
	and Dynamics of Biological Membranes},
  publisher = {Allen \& Unwin and The Solomon Press},
  year = {1985},
  author = {Brian L. Silver},
  address = {Publisher Creative Services Inc., Jamaica, New York}
}

@ARTICLE{STRE85,
  author = {M. L. Strenk and P. W. Westerman and J. W. Doane},
  title = {A model of orientational ordering in phosphatidylcholine bilayers
	based on conformational analysis of the glycerol backbone region},
  journal = BJ,
  year = {1985},
  volume = {48},
  pages = {765--773},
  annote = {requested Tx=19921106.}
}

@ARTICLE{TAVA85A,
  author = {Paul Tavan and Klaus Schulten and Wolfgang G{\"a}rtner and Dieter
	Oesterhelt},
  title = {Substituents at the {C}$_{13}$ Position of Retinal and their Influence
	on the Function of Bacteriorhodopsin},
  journal = BJ,
  year = {1985},
  volume = {47},
  pages = {349--356}
}

@ARTICLE{TAVA85,
  author = {Paul Tavan and Klaus Schulten and Dieter Oesterhelt},
  title = {The Effect of Protonation and Electrical Interactions on the Stereochemistry
	of Retinal {Schiff} Bases},
  journal = BJ,
  year = {1985},
  volume = {47},
  pages = {415--430}
}

@BOOK{THAN85,
  title = {Quantum Mechanics},
  publisher = {John Wiley \& Sons},
  year = {1985},
  author = {V. K. Thankappan},
  address = {New York}
}

@ARTICLE{TREU85,
  author = {Herbert Treutlein and Klaus Schulten},
  title = {Noise Induced Limit Cycles of the {B}onhoeffer--van~der~{P}ol Model
	of Neural Pulses},
  journal = BBG,
  year = {1985},
  volume = {89},
  pages = {710--718}
}

@ARTICLE{VALE85,
  author = {R.D. Vale and B.J. Schnapp and T. Mitchinson and E. Steuer and T.S.
	Reese and M.P. Sheetz},
  title = {Different axoplasmic proteins generate movement in opposite directions
	along microtubules {\em in vitro}},
  journal = CEL,
  year = {1985},
  volume = {43},
  pages = {623--632}
}

@ARTICLE{WATE85,
  author = {K.D. Watenpaugh},
  title = {Overview of Phasing by Isomorphous Replacement},
  journal = {Methods in Enzymology},
  year = {1985},
  volume = {115},
  pages = {3--15}
}

@ARTICLE{WELT85,
  author = {W. Welte and T. Wacker and M. Leis and W. Kreutz and J. Shiozawa
	and N. Gadon and G. Drews},
  title = {Crystallization of the photosynthetic light harvesting pigment-protein
	complex {B}800--850 of {{\em {R}hodopseudomonas capsulata}}},
  journal = {FEBS Lett. },
  year = {1985},
  volume = {182},
  pages = {260}
}

@ARTICLE{WERN85,
  author = {H-J.\ Werner and P.\ J.\ Knowles},
  title = {A Second Order Multiconfiguration {SCF} Procedure with Optimum Convergence},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {5053--5063}
}

@ARTICLE{WERN85X,
  author = { H.-J. Werner and P.~J. Knowles},
  title = {{A Second Order Multiconfiguration SCF Procedure with Optimum Convergence}},
  journal = JCP,
  year = {1985},
  volume = {82},
  pages = {5053--5063}
}

@ARTICLE{YAMA85,
  author = {K.~R.~Yamamoto},
  title = {Steroid receptor regulated transcription of specific genes and gene
	networks.},
  journal = ARG,
  year = {1985},
  volume = {19},
  pages = {209--252}
}

@ARTICLE{ZAUH85,
  author = {R.\ J.\ Zauhar and R.\ S.\ Morgan},
  title = {A New Method for Computing the Macromolecular Electric Potential},
  journal = JMB,
  year = {1985},
  volume = {186},
  pages = {815--820}
}

@ARTICLE{ZUBE85,
  author = {H. Zuber},
  title = {Structure and function of light-harvesting complexes and their polypeptides},
  journal = {Photochem. Photobiol.},
  year = {1985},
  volume = {42},
  pages = {821--825}
}

@ARTICLE{AGLO84,
  author = {A. U. Acu{\~n}a and J. Gonz{\'a}lez and M.P. Lillo and J.M. Ot{\'o}n},
  title = {The {U}{V} protein fluorescence of purple membrane and its apomembrane},
  journal = PCPB,
  year = {1984},
  volume = {40},
  pages = {351--359}
}

@ARTICLE{Aizu84,
  author = {K. Aizu},
  title = {Time-Reversal Invariance and Linear Multistep Methods for Integrating
	Dynamical Systems},
  journal = {J. Comput. Phys.},
  year = {1984},
  volume = {55},
  pages = {154--156}
}

@ARTICLE{BAAS84a,
  author = {T. Baasov and M. Sheves},
  title = {{C=C}-Streckschwingungsfrequenzen in Modellverbindungen der protonierten
	Schiff-Base des Retinals},
  journal = {Angewandte Chemie},
  year = {1984},
  volume = {96},
  pages = {786--787}
}

@ARTICLE{BAAS84b,
  author = {T. Baasov and M. Sheves},
  title = {Factors Affecting the Rate of Thermal Isomerization of 13-{\it cis\/}-Bacteriorhodopsin
	to All-Trans},
  journal = JACS,
  year = {1984},
  volume = {106},
  pages = {6840--6841}
}

@ARTICLE{BEREN84,
  author = {H.~J.~C.~Berendsen and J.~P.~M.~Postma and W.~F.~van~Gunsteren and
	A.~DiNola},
  title = {Molecular dynamics with coupling to external bath},
  journal = JCP,
  year = {1984},
  volume = {81},
  pages = {3684--3690}
}

@ARTICLE{BERE84,
  author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F.~van Gunsteren and
	A. DiNola and J.~R. Haak},
  title = {Molecular Dynamics with Coupling to an External Bath},
  journal = JCP,
  year = {1984},
  volume = {81},
  pages = {3684--3690},
  number = {8},
  keywords = {virial}
}

@ARTICLE{BPvD84,
  author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. van Gunsteren and
	A.~DiNola and J.~R. Haak},
  title = {Molecular Dynamics with Coupling to an External Bath},
  journal = {J. Chem.\ Phys.},
  year = {1984},
  volume = {81},
  pages = {3684--3690},
  number = {8}
}

@ARTICLE{BRAS84,
  author = {R. C. Brasch and H.-J. Weinmann and G. E. Wesbey},
  title = {Contrast-Enhanced {NMR} Imaging: Animal Studies Using Gd-DTPA Complex},
  journal = {AJR},
  year = {1984},
  volume = {{\bf 142}},
  pages = {625--630},
  brief = {(1st of Magin refs.) Gd-DTPA experimentally assessed as in vivo contrast
	agent. Concerns mostly contrast. Not esp. useful.},
  keywords = {paramagnetic contrast agent}
}

@ARTICLE{BRUN84,
  author = {Axel T. Br{\"u}nger and Charles L. {Brooks~I{}I{}I} and Martin Karplus},
  title = {Stochastic Boundary Conditions for Molecular Dynamics Simulations
	of {ST2} Water},
  journal = CPL,
  year = {1984},
  volume = {105},
  pages = {495--498},
  number = {5},
  annote = {THE reference for stochastic boundary; 98 water molecules in a sphere;
	mean density of water@283K is 0.0334molecules/A^3 = 0.9982g/cm^3;
	friction coefficient for oxygen of water; 51.3/ps; they have a more
	complicated boundary potential, not just simple harmonic: it looks
	more like a box with zero potential in the middle and a slowly increasing
	potential in the boundary region (like a vdW pot.) to confine the
	molecules in the volume; a fixed layer of molecules is found to be
	bad as it freezes free waters to it; dt=1fs; self diffusion coefficient
	of water@283K is 1.9*10^-5 cm^2/s},
  keywords = {reservoir region; reaction zone; deformable boundary}
}

@ARTICLE{BYUS84,
  author = {C. V. Byus and R. L. Lundak and R. M. Fletcher and W. R. Adey},
  title = {Alterations in Protein Kinase Activity Following Exposure of Cultured
	Human Lymphocytes to Modulated Microwave Fields},
  journal = {Bioelectromagnetics},
  year = {1984},
  volume = {5},
  pages = {341--351}
}

@ARTICLE{COLU84,
  author = {Lynne M. Coluccio and Lewis G. Tilney},
  title = {Phalloidin Enhances Actin Assembly by Preventing Monomer Dissociation},
  journal = JCB,
  year = {1984},
  volume = {99},
  pages = {529--535}
}

@ARTICLE{CROT84,
  author = {D.~M.~Crothers and H.~M.~Wu},
  title = {The locus of sequence--directed and protein--induced {\sc DNA} bending.},
  journal = NAT,
  year = {1984},
  volume = {308},
  pages = {509--513},
  annote = {have not read this paper but is cited in narduli's bending paper
	as origin of gel-assay mobilties determining bend angle, prokaryotic
	system with repressor or transactivator that bends DNA}
}

@BOOK{DEVA84,
  title = {Quantum-Mechanical Tunneling in Biological Systems},
  publisher = {Cambridge University press},
  year = {1984},
  author = {D. DeVault},
  address = {Cambridge, UK}
}

@ARTICLE{EISE84,
  author = {Eisenberg, D.},
  title = {Three-dimensional structure of membrane and surface proteins},
  journal = {Ann. Rev. Biochem.},
  year = {1984},
  volume = {53},
  pages = {595--523}
}

@ARTICLE{ELO84,
  author = {H. A. Elo and J. Korpella},
  title = {The occurrence and production of avidin: a new conception of the
	high-affinity biotin-binding protein},
  journal = {Comp. Biochem. Physiol.},
  year = {1984},
  volume = {78B},
  pages = {15--20},
  annote = {june 1}
}

@ARTICLE{EvMo84,
  author = {D.~J.~Evans and G.~P.~Moriss},
  title = {Non-{N}ewtonian Molecular Dynamics},
  journal = {Comput.\ Phys.\ Rep.},
  year = {1984},
  volume = {1},
  pages = {297--344}
}

@ARTICLE{GeWe84,
  author = {C.W. Gear and D.R. Wells},
  title = {Multirate linear multistep methods},
  journal = {BIT},
  year = {1984},
  volume = {24},
  pages = {484--502}
}

@ARTICLE{GERS84,
  author = {Lewis C. Gershman and Jay Newman and Lynn A. Selden and James E.
	Estes},
  title = {Bound-Cation Exchange Affects the Lag Phase in Actin Polymerization},
  journal = BCH,
  year = {1984},
  volume = {23},
  pages = {2199--2203}
}

@ARTICLE{GOUL84,
  author = {James L. Gould},
  title = {Magnetic Field Sensitivity in Animals},
  journal = {Annual Review of Physiology},
  year = {1984},
  volume = {46},
  pages = {585--598}
}

@ARTICLE{Gree84,
  author = {D. Greenspan},
  title = {Conservative Numerical Methods for $\ddot{x}= f(x)$},
  journal = {J. Comput. Phys.},
  year = {1984},
  volume = {56},
  pages = {28--41}
}

@ARTICLE{GROE84,
  author = {G.W.T. Groenendijk and W.J. De Grip and F.J.M. Daemen},
  title = {Rod Outer Segment Membranes: {G}ood Acceptors for Retinoids?},
  journal = {Vision Res.},
  year = {1984},
  volume = {24},
  pages = {1623--1627}
}

@INCOLLECTION{GRUE84,
  author = {D. W. R. Gruen and E. H. B. de Lacey},
  title = {The packing of amphiphile chains in micelles and bilayers},
  booktitle = {Surfactants in Solution},
  publisher = {Plenum Publishing Corp.},
  year = {1984},
  editor = {K. L. Mittal and B. Lindman},
  volume = {1},
  pages = {279--306},
  address = {New York},
  annote = {requested Tx=19920902.}
}

@ARTICLE{GUHA84,
  author = {F. Guharay and F. Sachs},
  title = {Stretch-activated single ion channel currents in tissue-cultured
	embryonic chick skeletal muscle},
  journal = {J. Physiol. (Lond.)},
  year = {1984},
  volume = {352},
  pages = {685--701},
  annote = {First discovery of MS channels}
}

@ARTICLE{GUNS84,
  author = {W. F. van Gunsteren and H. J. C. Berendsen and F. Colonna and D.
	Perahia and J. P. Hollenberg and D. Lellouch},
  title = {On Searching Neighbors in Computer Simulations of Macromolecular
	Systems},
  journal = JCC,
  year = {1984},
  volume = {5},
  pages = {272--279},
  number = {3}
}

@ARTICLE{HARB84,
  author = {G. Harbison and O. Smith and J. Pardoen and C. Winkel and J. Lugtenburg
	and J. Herzfeld and R. Mathies and R. Griffin},
  title = {Dark-adapted bacteriorhodopsin contains 13-{\it cis},15-{\it syn}
	and all-{\it trans},15-{\it anti} retinal Schiff bases.},
  journal = PNAS,
  year = {1984},
  volume = {81},
  pages = {1706--1709}
}

@ARTICLE{HILD84,
  author = {P. Hildebrandt and M. Stockburger},
  title = {Role of Water in Bacteriorhodopsin's Chromophore: Resonance {Raman}
	Study},
  journal = BCH,
  year = {1984},
  volume = {23},
  pages = {5539--5548}
}

@INPROCEEDINGS{HLAD84,
  author = {S.B. Hladky and D.A. Haydon},
  title = {Ion movements in gramicidin channels.},
  booktitle = {Current topics in membranes and transport},
  year = {1984},
  editor = {F. Bronner and W.D. Stein},
  volume = {21},
  pages = {327--372},
  address = {New York},
  publisher = {Academic press}
}

@ARTICLE{HOUS84,
  author = {W. House},
  title = {{NMR} microscopy},
  journal = {IEEE Trans. Nuc. Sci.},
  year = {1984},
  volume = {31},
  pages = {570}
}

@ARTICLE{KEEP84,
  author = {J. W. Keepers and T. L. James},
  title = {A Theoretical Study of Distance Determinations From {NMR}. {T}wo
	Dimensional Nuclear {O}verhauser Effect Spectra},
  journal = JMR,
  year = {1984},
  volume = {57},
  pages = {404--426}
}

@ARTICLE{KIM84,
  author = {P. S. Kim and R. L. Baldwin},
  title = {A Helix Stop Signal in the Isolated {S}-Peptide of Ribonuclease~{A}},
  journal = NAT,
  year = {1984},
  volume = {307},
  pages = {329--334}
}

@ARTICLE{KRAM84,
  author = {H.J.M. Kramer and R. van Grondelle and C. N. Hunter and W.H.J. Westerhuis
	and J. Amesz},
  title = {Pigment organization of the B800--850 antenna complex of {\em {R}hodopseudomonas
	sphaeroides}},
  journal = {Biochim.~Biophys.~Acta},
  year = {1984},
  volume = {765},
  pages = {156--165}
}

@BOOK{KUCH84,
  title = {{T}aschenbuch der {P}hysik},
  publisher = {Verlag Harri Deutsch},
  year = {1984},
  author = {Horst Kuchling},
  address = {Thun, Frankfurt/Main},
  edition = {5}
}

@ARTICLE{KURR84,
  author = {H. Kurreck and M. Bock and N. Bretz and M. Elsner and H. Kraus and
	W. Lubitz and F. M{\"u}ller and J. Geissler and P.M.H. Kroneck},
  title = {Fluid solution and solid-state electron nuclear double resonance
	studies of flavin model compounds and flavoenzymes},
  journal = {J.~Am.~Chem.~Soc.},
  year = {1984},
  volume = {106},
  pages = {737--746}
}

@BOOK{LAND84,
  title = {Mechanik},
  publisher = {Akademie-Verlag},
  year = {1984},
  author = {L. D. Landau and E. M. Lifschitz},
  volume = {1},
  series = {Lehrbuch der Theoretischen Physik},
  address = {Berlin},
  edition = {11}
}

@ARTICLE{LEE84,
  author = {C.Y. Lee and J.A. McCammon and P.J. Rossky},
  title = {The structure of liquid water at an extended hydrophobic surface},
  journal = JCP,
  year = {1984},
  volume = {80},
  pages = {4448}
}

@ARTICLE{LESK84,
  author = {Arthur M. Lesk and Cyrus Chothia},
  title = {Mechanisms of Domain Closure in Proteins},
  journal = JMB,
  year = {1984},
  volume = {174},
  pages = {175--191}
}

@ARTICLE{LEVI84,
  author = {Michael Levine and David Stuart and John Williams},
  title = {A Method for the Systematic Comparison of Three-Dimensional Structures
	of Proteins and Some Results},
  journal = ACA,
  year = {1984},
  volume = {40},
  pages = {600--610}
}

@ARTICLE{LIBO84,
  author = {Liboff and Williams and Strong and Wistar},
  title = {Time-Varying Magnetic Fields: Effect on {DNA} Synthesis},
  journal = SCI,
  year = {1984},
  volume = {223},
  pages = {818--820}
}

@INPROCEEDINGS{PHER84,
  author = {A. McPherson and G.D. Brayer},
  title = {The Gene 5 Protein and its Molecular Complexes},
  booktitle = {Biological Macromolecules and Assemblies},
  year = {1984},
  editor = {F.A. Jurnak and A. McPherson},
  volume = {2},
  pages = {324--391},
  address = {New York},
  publisher = {John Wiley and Sons}
}

@ARTICLE{Meny84,
  author = {C. R. Menyuk},
  title = {Some Properties of the Discrete \mbox{Hamiltonian} Method},
  journal = {Physica D},
  year = {1984},
  volume = {11},
  pages = {109--129}
}

@ARTICLE{MERZ84,
  author = {M. M. Merzenich and others},
  title = {Somatosensory Cortical Map Changes Following Digit Amputation in
	Adult Monkeys},
  journal = {J. Comp. Neurology},
  year = {1984},
  volume = {224},
  pages = {591--605}
}

@ARTICLE{MOUR84,
  author = {O.G. Mouritsen and M. Bloom},
  title = {Mattress model of lipid-protein interactions in membranes},
  journal = BJ,
  year = {1984},
  volume = {46},
  pages = {141}
}

@ARTICLE{NADL84,
  author = {Walter Nadler and Klaus Schulten},
  title = {Theory of {M}\"ossbauer Spectra of Proteins Fluctuating between Conformational
	Substates},
  journal = PNAS,
  year = {1984},
  volume = {81},
  pages = {5719--5723}
}

@ARTICLE{NAGE84,
  author = {S. R. Nagel and G. S. Grest and A. Rahman},
  title = {Phonon Localization and Anharmonicity in Model Glasses},
  journal = PRL,
  year = {1984},
  volume = {53},
  pages = {368--371},
  number = {4}
}

@ARTICLE{NEUM84,
  author = {M. Neumann and O. Steinhauser and G. S. Pawley},
  title = {Consistent calculation of the static and fregquency-dependent dielectric
	constant in computer simulations},
  journal = {Mol. Physicsa},
  year = {1984},
  volume = {52},
  pages = {97--113}
}

@ARTICLE{NEWT84,
  author = {D.L. Newton and M.D. Oldewurtel and M.H. Krinks and J. Shiloach and
	C.B. Klee},
  title = {Agonist and Antagonist Properties of Calmodulin Fragments},
  journal = JBC,
  year = {1984},
  volume = {259},
  pages = {4419--4426}
}

@ARTICLE{NICH84,
  author = {A. V. Nichols and E. L. Gong and P. J. Blanche and T. M. Forte and
	V. G. Shore},
  title = {Interaction of Model Discoidal Complexes of Phosphatidylcholine and
	Apolipoprotein {A-I} Plasma Components},
  journal = BBA,
  year = {1984},
  volume = {793},
  pages = {325--337}
}

@ARTICLE{NILS84,
  author = {L.~Nilsson and M.~Karplus},
  title = {Energy functions for energy minimization and dynamics of nucleic
	acids.},
  journal = JCC,
  year = {1984},
  volume = {1},
  pages = {591--616}
}

@ARTICLE{NORT84,
  author = {Scott H. Northrup},
  title = {Molecular Mechanics of Kink Formation in Lipid Monolayers},
  journal = JPC,
  year = {1984},
  volume = {88},
  pages = {3441--3446},
  annote = {800 kcal/mol harmonic restraint forces used to anchor lipid chains;
	chain spacing in hexagonal grid of 4.6AA; united atom model; only
	chains, no headgroups simulated; kinks are introduced by an external
	potential; g_+: gauche: 300^o; g_-: antigauche: 60^o; although only
	one angle was tweeked, the other dihedral followed by itself resulting
	in a crankshaft motion; very reduced simulation of 61 chains},
  keywords = {membrane; gel state; liquid crystall state; phase transition; crankshaft
	motion},
  suggestions = {What do we see in our simulation? Crankshaft movement or just isolated
	t->g transitions?}
}

@ARTICLE{NoAM84,
  author = {S. H. Northrup and S. A. Allison and J. A. McCammon},
  title = {Brownian Dynamics Simulation of Diffusion-Influenced Bimolecular
	Reactions},
  journal = {J. Chem.\ Phys.},
  year = {1984},
  volume = {80},
  pages = {1517--1524},
  number = {4}
}

@ARTICLE{Nose84,
  author = {Shuichi Nos{\'e}},
  title = {A unified formulation of the constant temperature molecular dynamics
	methods},
  journal = {J. Chem. Phys.},
  year = {1984},
  volume = {81},
  pages = {511--519},
  number = {1},
  annote = {analytical treatment of three constant temperature simulations}
}

@ARTICLE{NoBK84,
  author = {J. Novotny and R. Bruccoleri and M. Karplus},
  title = {An Analysis of Incorrectly Folded Proteins---Implications for Structure
	Prediction},
  journal = JMB,
  year = {1984},
  volume = {177},
  pages = {787--818},
  number = {4},
  annote = {hard for traditional MD force fields to discriminate native structures,
	cited in Zhan99}
}

@BOOK{ORBA84,
  title = {Neuronal Operations in the Visual Cortex},
  publisher = {Springer-Verlag},
  year = {1984},
  author = {G. A. Orban},
  address = {New York}
}

@ARTICLE{PABO84,
  author = {C.~O.~Pabo and R.~T.~Sauer},
  title = {Protein-{DNA} Recognition},
  journal = ARB,
  year = {1984},
  volume = {53},
  pages = {293--321}
}

@ARTICLE{PaPe84,
  author = {A. V. Panfilov and A. M. Pertsov},
  title = {Vortex ring in a three-dimensional active medium described by reaction-diffusion
	equations},
  journal = {Dokl. Akad. Nauk},
  year = {1984},
  volume = {274},
  pages = {1500--1503}
}

@ARTICLE{PARO84,
  author = {L. A. Parodi and R. H. Lozier and S. M. Bhattacharjee and J. F. Nagle},
  title = {Testing Kinetic Models for the Bacteriorhodopsin Photocycle-{II}.
	Inclusion of an {O} to {M} Back Reaction},
  journal = PCPB,
  year = {1984},
  volume = {40},
  pages = {501--506}
}

@ARTICLE{PETS84,
  author = {Gregory A. Petsko and Dagmar Ringe},
  title = {Fluctuations in Protein Structure from {X}-ray Diffraction},
  journal = ARBPB,
  year = {1984},
  volume = {13},
  pages = {331--371},
  annote = {review; precision of B-facotrs; plot B-factors over backbone atom
	numbers; comparison with MD simulations},
  keywords = {Debye-Waller-factor; lattice disorder}
}

@ARTICLE{RICH84,
  author = {Timothy J.\ Richmond},
  title = {Solvent Accessible Surface Area and Excluded Volume in Proteins},
  journal = JMB,
  year = {1984},
  volume = {178},
  pages = {63--90}
}

@ARTICLE{RICH84A,
  author = {T.~J.~Richmond and J.~T.~Finch and B.~Rushton and D.~Rhodes and A.~Klug},
  title = {Structure of the nucleosome core particle at {7\,\AA} resolution},
  journal = NAT,
  year = {1984},
  volume = {311},
  pages = {532--537}
}

@BOOK{SALI84,
  title = {Spin Polarization and Magnetic Field Effects in Radical Reactions},
  publisher = {Elsevier},
  year = {1984},
  editor = {Y.N. Molin},
  author = {K.M. Salikhov and Y.N. Molin and R.Z. Sagdeev and A.L. Buchanenko},
  volume = {22},
  address = {Budapest},
  booktitle = {Studies in Physical and Theoretical Chemistry}
}

@ARTICLE{SCHE84A,
  author = {A. Scherz and W. W. Parson},
  title = {Oligomers of bacteriochlorophyll and bacteriopheophytin with spectroscopic
	properties resembling those found in photosynthetic bacteria},
  journal = BBA,
  year = {1984},
  volume = {766},
  pages = {653--665}
}

@ARTICLE{SCHU84,
  author = {Klaus Schulten},
  title = {Ensemble Averaged Spin Pair Dynamics of Doublet and Triplet Molecules},
  journal = JCP,
  year = {1984},
  volume = {80},
  pages = {3668--3679}
}

@INCOLLECTION{SCHU84A,
  author = {Klaus Schulten and Axel Br{\"u}nger and Walter Nadler and Zan Schulten},
  title = {Generalized Moment Description of {B}rownian Dynamics in Biological
	Systems},
  booktitle = {Synergetics --- From Microscopic to Macroscopic Order},
  publisher = {Springer},
  year = {1984},
  editor = {E. Frehland},
  pages = {80--89}
}

@INCOLLECTION{SCHU84B,
  author = {Klaus Schulten and Zan Schulten and Paul Tavan},
  title = {An Isomerization Model for the Pump Cycle of Bacteriorhodo\-psin},
  booktitle = {Information and Energy Transduction in Biological Membranes},
  publisher = {Allan R.\ Liss, Inc.},
  year = {1984},
  editor = {L. Bolis and E. J. M. Helmreich and H. Passow},
  pages = {113--131},
  address = {New York}
}

@ARTICLE{SCHU84C,
  author = {Klaus Schulten and Albert Weller},
  title = {Magnetfeldeffekte in {C}hemie und {B}iologie},
  journal = DU,
  year = {1984},
  volume = {25/26},
  pages = {779--783}
}

@ARTICLE{SEDD84,
  author = {J.M. Seddon and G. Cevc and R.D. Kaye and D. Marsh},
  title = {{X}-ray diffraction study of the polymorphism of hydrated diacyl-
	and dialkylphosphotidylethanolamine},
  journal = BCH,
  year = {1984},
  volume = {23},
  pages = {2634--2644}
}

@ARTICLE{SEMM84,
  author = {P. Semm and D. Nohr and C. Demaine and W. Wiltschko},
  title = {Neural basis of the magnetic compass: interactions of visual, magnetic
	and vestibular inputs in the pigeon's brain},
  journal = {J. Comp. Physiol. A},
  year = {1984},
  volume = {155},
  pages = {283--288}
}

@ARTICLE{SHEV84A,
  author = {M. Sheves and T. Baasov},
  title = {Factors Affecting the Rate of Thermal Isomerization of 13-{\it cis}-{Bacteriorhodopsin}
	to All-{Trans}},
  journal = JACS,
  year = {1984},
  volume = {106},
  pages = {6840--6841}
}

@ARTICLE{SHEV84,
  author = {M. Sheves and T. Baasov and N. Friedman and M. Ottolenghi and R.
	{Feinmann-Weinberg} and V. Rosenbach and B. Ehrenberg},
  title = {On the Binding-Site of Bacteriorhodopsin\ --\ A Study with Artificial
	Pigments},
  journal = JACS,
  year = {1984},
  volume = {106},
  pages = {2435--2437}
}

@ARTICLE{SING84,
  author = {U. C. Singh and P. A. Kollman},
  title = {An Approach to Computing Electrostatic Charges for Molecules},
  journal = JCC,
  year = {1984},
  volume = {5},
  pages = {129--145}
}

@ARTICLE{SMIT84,
  author = {S. Smith and A. Myers and J. Pardoen and C. Winkel and P. Mulder
	and J. Lugtenburg and R. Mathies},
  title = {Determination of retinal Schiff base configuration in bacteriorhodopsin.},
  journal = BIO,
  year = {1984},
  volume = {81},
  pages = {2055--2059}
}

@ARTICLE{SUSS84,
  author = {D.J. Sussman and J.R. Sellers and P. Flicker and E.Y. Lai and L.E.
	Cannon and A.G. Szent-Gy{\"o}rgyi and C. Fulton},
  title = {Actin of {{\em Naegleria gruberi}}},
  journal = JBC,
  year = {1984},
  volume = {259},
  pages = {7349--7354}
}

@ARTICLE{TAVA84,
  author = {Paul Tavan and Klaus Schulten},
  title = {The Effect of Protonation on the Thermal Isomerization of Stilbazolium
	Betaines},
  journal = CPL,
  year = {1984},
  volume = {110},
  pages = {191--195}
}

@BOOK{TYRE84,
  title = {Diffusion in Electrolytes},
  publisher = {Butterworths},
  year = {1984},
  author = {H. J. V. Tyrell and K. R. Harris},
  address = {London},
  booktitle = {Diffusion in Liquids},
  chapter = {8}
}

@ARTICLE{WARS84,
  author = {A. Warshel and S.\ T.\ Russell},
  title = {Calculations of Electrostatic Interactions in Biological Systems
	and in Solutions},
  journal = QRB,
  year = {1984},
  volume = {17},
  pages = {283--422}
}

@ARTICLE{WEBE84,
  author = {I.~T.~Weber and T.~A.~Steitz},
  title = {Model of specific complex between catabolite gene activator protein
	and {B--DNA} suggested by electrostatic complementarity},
  journal = PNAS,
  year = {1984},
  volume = {81},
  pages = {3973-- },
  annote = { CAP forms a dimer and is activated by allosteric effector cAMP CAP
	falls in helix-turn-helix motiff, very similar to CRO and lambda
	cI repressor, but lambda and CAP have helix parallel to bases and
	doesn't protrude into groove as far. For CRO the helix is parallel
	to major groove which is inclined about 32deg to plane of bases.
	a. this was a model building of {DNA}and protein complex b. bend
	20bp of {DNA}by radius of curvature of 70deg around the protein c.
	used solvent accessibiltiy modified Tanford-Kirkwood theory to cal
	electrostatic charge distrib in order to fit protein and DNA d. refs
	to free energy calcs and real theory of bending e. refs ethylation
	(phosphates), methylation(guanines), crosslinking by UV irradiation,
	and mutations as experimental support for model f. {DNA}binding domains
	of CAP dimer are not precisely 2 fold related, therefore contacts
	to {DNA}not precisely 2fold. }
}

@ARTICLE{WEIN84,
  author = {S.P.~Weiner and P.A.~Kollman and D.A.~Case and U.C.~Singh and C.~Ghio
	and G.~Alagona and J.~Profeta and P.Weiner},
  title = {A new force field for molecular mechanical simulation of nucleic
	acids and proteins.},
  journal = JAC,
  year = {1984},
  volume = {106},
  pages = {765--784}
}

@ARTICLE{WEIN84A,
  author = {S.P.~Weiner and P.A.~Kollman and D.A.~Case and U.C.~Singh and C.~Ghio
	and G.~Alagona and J.~Profeta and P.Weiner},
  title = {A New Force Field for Molecular Mechanical Simulation of Nucleic
	Acids and Proteins},
  journal = JACS,
  year = {1984},
  volume = {106},
  pages = {765--784}
}

@ARTICLE{WOOD84,
  author = {N. W. T. Woodbury and W. W. Parson},
  title = {Nanosecond Fluorescence from Isolated Photosynthetic Reaction Centers
	of {\em Rhodopseudomonas sphaeroides}},
  journal = BBA,
  year = {1984},
  volume = {767},
  pages = {345--361}
}

@PHDTHESIS{HOCH83,
  author = {Jeffrey Craig Hoch},
  title = {The Influence of Protein Structure and Dynamics on {NMR} Parameters},
  school = {Harvard},
  year = {1983},
  month = JAN
}

@ARTICLE{Aizu83,
  author = {K. Aizu},
  title = {Application of Time Reversal Invariance to Numerical Experiments
	of Many Body Systems},
  journal = {Prog. Theoretical Phys.},
  year = {1983},
  volume = {70},
  pages = {106--118},
  number = {1}
}

@ARTICLE{ALSI83,
  author = {A. Alsina and O. Valls and G. Pieroni and R. Verger and S. Garc\'ia},
  title = {Lipolysis by phospholipase {A$_2$} of monomolecular mixed films of
	natural lipids},
  journal = {Colloid \& polymer science},
  year = {1983},
  volume = {261},
  pages = {923--928},
  annote = {PLA2 on monolayePLA2 on monolayerr}
}

@ARTICLE{Ande83,
  author = {H.~C. Andersen},
  title = {Rattle: A `Velocity' Version of the {S}hake Algorithm for Molecular
	Dynamics Calculations},
  journal = {J. Comput.\ Phys.},
  year = {1983},
  volume = {52},
  pages = {24--34}
}

@ARTICLE{BLUM83,
  author = {A. Blume},
  title = {Apparent molar heat capacities of phospholipids in aqeous dispersion,
	effects of chain length and head group structure},
  journal = BCH,
  year = {1983},
  volume = {22},
  pages = {5436}
}

@ARTICLE{BOXE83,
  author = {S.G. Boxer and C.E.D. Chidsey and Mark.G. Roelofs},
  title = {Magnetic field effects on reaction rates in the solid state: An example
	from photosynthetic reaction centers},
  journal = {Ann.~Rev.~Phys.~Chem.},
  year = {1983},
  volume = {34},
  pages = {389--417}
}

@ARTICLE{BroK83a,
  author = {B.~Brooks and M.~Karplus},
  title = {Harmonic dynamics of proteins:{\,}{N}ormal modes and fluctuations
	in bovine pancreatic trypsin inhibitor},
  journal = PNAS,
  year = {1983},
  volume = {80},
  pages = {6571-6575}
}

@ARTICLE{Broo83,
  author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States
	and S. Swaminathan and M. Karplus},
  title = {{CHARMM:} {A} Program for Macromolecular Energy, Minimization, and
	Dynamics Calculations},
  journal = JCC,
  year = {1983},
  volume = {4},
  pages = {187--217},
  number = {2}
}

@ARTICLE{BROO83A,
  author = {C.~L.~{Brooks~I{}I{}I} and M.~Karplus},
  title = {Deformable stochastic boundaries in molecular dynamics},
  journal = JCP,
  year = {1983},
  volume = {79},
  pages = {6312--6325},
  number = {12},
  annote = {title says it all, ref BERE84,NOSE84,TOBI94}
}

@ARTICLE{BROW83,
  author = {Michael F. Brown and Anthony A. Ribeiro and Gerald D. Williams},
  title = {New view of lipid bilayer dynamics from $^2${H} and $^{13}${C} {NMR}
	relaxation time measurements},
  journal = PNAS,
  year = {1983},
  volume = {80},
  pages = {4325--4329},
  annote = {experimental},
  keywords = {frequency dependence; order fluctuations; vesicles; microviscosity;
	liquid crystals; membrane; dipalmitoylphsophatidylcholine DPPC}
}

@ARTICLE{BRUN83,
  author = {Axel Br{\"u}nger and Zan Schulten and Klaus Schulten},
  title = {A Network Thermodynamic Investigation of Stationary and Non-Stationary
	Proton Transport through Proteins},
  journal = ZPC,
  year = {1983},
  volume = {NF136},
  pages = {1--63}
}

@ARTICLE{CALD83A,
  author = {A. O. Cardeira and A. J. Leggett},
  title = {Quantum Tunnelling in a Dissipative System},
  journal = {J. Ann. Phys.(N.Y.)},
  year = {1983},
  volume = {149},
  pages = {374--456}
}

@ARTICLE{CALD83B,
  author = {A. O. Cardeira and A. J. Leggett},
  title = {Path Integral Approach to Quantum Brownian Motion},
  journal = {Physica A},
  year = {1983},
  volume = {121},
  pages = {587--616}
}

@ARTICLE{CONN83,
  author = {Michael L.\ Connolly},
  title = {Solvent-Accessible Surfaces of Proteins and Nucleic Acids},
  journal = SCI,
  year = {1983},
  volume = {221},
  pages = {709--713}
}

@ARTICLE{COOP83,
  author = {John A. Cooper and E. Loren Buhle and Simon B. Walker and Tian Y.
	Tsong and Thomas D. Pollard},
  title = {Kinetic Evidence for a Monomer Activation Step in Actin Polymerization},
  journal = BCH,
  year = {1983},
  volume = {22},
  pages = {2193--2202}
}

@ARTICLE{CORE83,
  author = {D. P. Corey and A. J. Hudspeth},
  title = {Kinetics of the receptor current in bullfrog saccular hair cells},
  journal = JN,
  year = {1983},
  volume = {3},
  pages = {962--976},
  annote = {MS channels in eukaryotes}
}

@ARTICLE{CREM83,
  author = {G. Cremer-Bartels and K. Krause and H. J. Kuchle},
  title = {Influence of low magnetic-field-strength variations on the retina
	and pineal gland of quail and humans},
  journal = {Graefe's Arch Clin Exp Opthalmol},
  year = {1983},
  volume = {220},
  pages = {248--252}
}

@INPROCEEDINGS{DENN83,
  author = {E. A. Dennis},
  title = {Phospholipases},
  booktitle = {The enzymes},
  year = {1983},
  volume = {XVI},
  pages = {307--353},
  publisher = {Academic Press, Inc.},
  annote = {Review article}
}

@ARTICLE{DIJK83,
  author = {B. W. Dijkstra and K. H. Kalk and W. J. H. Hol and J. Drenth},
  title = {Structure of Porcine Pancreatic Phospholipase~{A}$_2$ at {2.6\,\AA\,}
	Resolution and Comparison with Bovine Phospholipase~{A}$_2$},
  journal = JMB,
  year = {1983},
  volume = {147},
  pages = {97--123}
}

@ARTICLE{EDEL83,
  author = {H. Edelsbrunner and D. G. Kirkpatrick and R. Seidel},
  title = {On the Shape of a Set of Points in the Plane},
  journal = {IEEE Transactions on Information Theory},
  year = {1983},
  volume = {IT-29},
  pages = {551--559}
}

@ARTICLE{EDHO83,
  author = {O. Edholm and H. J. C. Berendsen and P. van der Ploeg},
  title = {Conformational entropy of a bilayer membrane derived from a molecular
	dynamics simulation},
  journal = MP,
  year = {1983},
  volume = {48},
  pages = {379--388},
  number = {2},
  annote = {80ps; 128 alkane chains with 9 hydrocarbon groups+head group; data
	saved every 32fs},
  keywords = {simulation; kink-disorder; main phase transition; entropy},
  suggestions = {compute entropy and free energy}
}

@ARTICLE{ELLI83,
  author = {J.R. Elliot and D. Needham and J.P. Dilger and D.A. Haydon},
  title = {The effects of bilayer thickness and tension on gramicidin single-channel
	life time},
  journal = BBA,
  year = {1983},
  volume = {735},
  pages = {95--103}
}

@BOOK{GARD83,
  title = {Handbook of Stochastic Methods},
  publisher = {Springer},
  year = {1983},
  author = {C. W. Gardiner},
  address = {New York}
}

@ARTICLE{GTWK83,
  author = {Getzoff, E. D. and Tainer, J. A. and Weiner, P. K. and Kollman, P.
	A. and Richardson, J. S. and Richardson, D. C},
  title = {Electrostatic Recognition Between Superoxide and Copper, Zinc Superoxide
	Dismutase},
  journal = NAT,
  year = {1983},
  volume = {306},
  pages = {287}
}

@ARTICLE{Glas83,
  author = {?? L.J. Glass},
  title = {temperature echos},
  journal = {Physics Today},
  year = {1983},
  volume = {??}
}

@BOOK{GuHo83,
  title = {Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector
	Fields},
  publisher = {Springer-Verlag},
  year = {1983},
  author = {J. Guckenheimer and P. Holmes},
  address = {New York},
  nremark = {531.322G933N, discusses averaging}
}

@INCOLLECTION{GUNS83,
  author = {W.\ F.\ van Gunsteren and H.\ J.\ C.\ Berendsen},
  title = {Stochastic Dynamics of Polymers},
  booktitle = {The Physics of Superionic Conductors and Electrode Materials},
  publisher = {Plenum Press},
  year = {1983},
  editor = {J. W. Perram},
  volume = {92},
  series = NASB,
  pages = {241},
  address = {New York}
}

@ARTICLE{Jorg83,
  author = {W.~L.~Jorgensen and J.~Chandrasekhar and J.~D.~Madura and R.~W.~Impey
	and M.~L.~ Klein},
  title = {Comparison of Simple Potential Functions for Simulating Liquid Water},
  journal = JCP,
  year = {1983},
  volume = {79},
  pages = {926--935},
  annote = {Many properties are analyzed and compared to experimental values},
  keywords = {Water model: BF, SPC, ST2, TIPS2, TIP3P, TIP4P}
}

@ARTICLE{KABS83,
  author = {W. Kabsch and C. Sander},
  title = {How Good are Predictions of Protein Secondary Structure?},
  journal = FEBS,
  year = {1983},
  volume = {155},
  pages = {179}
}

@ARTICLE{KABS83b,
  author = {W. Kabsch and C. Sander},
  title = {Dictionary of protein secondary structure: pattern recognition of
	hydrogen-bonded and geometrical features},
  journal = BP,
  year = {1983},
  volume = {22},
  pages = {2577--637}
}

@ARTICLE{KAKI83,
  author = {T. Kakitani and H. Kakitani and H. Rodman and B. Honig and R. Callender},
  title = {Correlation of Vibrational Frequencies with Absorption Maxima in
	Polyenes, Rhodopsin, Bacteriorhodopsin, and Retinal Analogs},
  journal = JPC,
  year = {1983},
  volume = {87},
  pages = {3620--3628}
}

@ARTICLE{KARP83,
  author = {M. Karplus and J. A. McCammon},
  title = {Dynamics of Proteins: Elements and Function},
  journal = {Ann. Rev. Biochem.},
  year = {1983},
  volume = {53},
  pages = {263--300}
}

@ARTICLE{KIRK83,
  author = {S. Kirkpatrick and C. D. Gelatt, Jr. and M. P. Vecchi},
  title = {Optimization by Simulated Annealing},
  journal = SCI,
  year = {1983},
  volume = {220},
  pages = {671--680}
}

@BOOK{KOHO83,
  title = {Self-Organization and Associative Memory},
  publisher = {Springer-Verlag},
  year = {1983},
  author = {T. Kohonen},
  address = {Berlin}
}

@ARTICLE{LAMM83,
  author = {Gene Lamm and Klaus Schulten},
  title = {Extended {B}rownian Dynamics: {II}.\ {R}eactive, Nonlinear Diffusion},
  journal = JCP,
  year = {1983},
  volume = {78},
  pages = {2713--2734}
}

@ARTICLE{Levi83,
  author = {Michael Levitt},
  title = {Molecular Dynamics of Native Protein},
  journal = JMB,
  year = {1983},
  volume = {168},
  pages = {595--620},
  annote = {introduction with groundlaying references; explains in (boring) detail
	what kind of MD, parameters etc. he used; timestep: 2fs; small violations
	of energy conservation are removed by temperature rescaling},
  keywords = {BPTI; H-bonds explicite/implicite; conjugate gradient energy minimization}
}

@ARTICLE{LEVI83b,
  author = {M.~Levitt},
  title = {Protein folding by restrained energy minimization and molecular dynamics},
  journal = {J. Mol. Biol.},
  year = {1983},
  volume = {170},
  pages = {723--764}
}

@ARTICLE{LYLE83,
  author = {D. B. Lyle and P. Schechter and W. R. Adey and R. L. Lundak},
  title = {Suppression of T-Lymphocyte Cytotoxicity Following Exposure to Sinusoidally
	Amplitude-Modulated Fields},
  journal = {Biolelectromagnetics},
  year = {1983},
  volume = {4},
  pages = {281--292}
}

@ARTICLE{MERZ83,
  author = {M. M. Merzenich and others},
  title = {Progression of Change Following Median Nerve Section in the Cortical
	Representation of the Hand in Areas~3b and~1 in Adult Owl and Squirrel
	Monkeys},
  journal = {Neuroscience},
  year = {1983},
  volume = {10},
  pages = {639--665}
}

@ARTICLE{NADL83,
  author = {Walter Nadler and Klaus Schulten},
  title = {Generalized Moment Expansion for the {M}\"ossbauer Spectrum of {B}rownian
	Particles},
  journal = PRL,
  year = {1983},
  volume = {51},
  pages = {1712--1715}
}

@ARTICLE{NAGE83,
  author = {S. R. Nagel and G. S. Grest and A. Rahman},
  title = {Quench Echoes},
  journal = {Physics Today},
  year = {1983},
  volume = OCT,
  pages = {24--32}
}

@ARTICLE{NAGL83,
  author = {John F. Nagle and Stephanie Tristram-Nagle},
  title = {Hydrogen Bonded Chain Mechanism for Proton Conduction and Proton
	Pumping},
  journal = JMEB,
  year = {1983},
  volume = {74},
  pages = {1--14}
}

@ARTICLE{PETE83,
  author = {D. C. Petersen},
  title = {The water permeability of the monolein/triolein bilayer membrane},
  journal = BBA,
  year = {1983},
  volume = {734},
  pages = {201--209},
  annote = {requested Tx=19920908.}
}

@ARTICLE{PLOE83,
  author = {P. van der Ploeg and H. J. C. Berendsen},
  title = {Molecular dynamics of a bilayer membrane},
  journal = MP,
  year = {1983},
  volume = {49},
  pages = {233--248},
  number = {1},
  annote = {surface area per head group: 25--27.6A^2; periodic boundary; 2 x
	64 decane molecules; 4 x 80ps simulations; united atoms; SHAKE; dt=8fs;
	analysis of MD data; many ideas on what to analyze},
  keywords = {order parameters; density profile; lateral pressure; translational
	diffusion},
  suggestions = {many ideas on what to analyze}
}

@ARTICLE{Ruth83,
  author = {R. D. Ruth},
  title = {A Canonical Integration Technique},
  journal = {IEEE Trans.\ Nucl.\ Sci.},
  year = {1983},
  volume = {30},
  pages = {2669--2671},
  number = {4}
}

@INCOLLECTION{SCHU83,
  author = {Klaus Schulten},
  title = {Ensemble Averaged Spin Pair Dynamics of Doublet and Triplet Molecules},
  booktitle = {Organic Molecular Aggregates},
  publisher = {Springer},
  year = {1983},
  editor = {P. Reineker and H. Haken and H. C. Wolf},
  pages = {76--87}
}

@ARTICLE{SELD83,
  author = {Lynn A. Selden and James E. Estes and Lewis C. Gershman},
  title = {The tightly bound divalent cation regulates actin polymerization},
  journal = BBRC,
  year = {1983},
  volume = {116},
  pages = {478--485}
}

@INCOLLECTION{SMIT83,
  author = {S. Smith and M. Braiman and R. Mathies},
  title = {Time-Resolved Resonance Raman Spectroscopy of the $\rm K_{610}$ and
	$\rm O_{640}$ Photointermediates of Bacteriorhodopsin},
  booktitle = {Time-Resolved Vibrational Spectroscopy},
  publisher = {Academic Press},
  year = {1983},
  pages = {219--230}
}

@ARTICLE{SMIT83b,
  author = {Smith,S.O. and Pardoen,J.A. and Mulder,P.P.J. and Curry,B. and Lugtenburg,J.},
  title = {Chromophore structure in bacteriorhodopsin's {O}$_{640}$ photointermediate},
  journal = BCH,
  year = {1983},
  volume = {22},
  pages = {6141--6148}
}

@ARTICLE{SMIT83A,
  author = {S. O. Smith and R. Mathies},
  title = {Structure of the Chromophore in the {O}-640 Intermediate of Bacteriorhodopsin},
  journal = BJ,
  year = {1983},
  volume = {41},
  pages = {13a},
  annote = {for 27th Annual Meeting of the Biophysical Society, San Diego}
}

@ARTICLE{TaNW83,
  author = {Hideki Tanaka and Koichiro Nakanishi and Nobuatsu Watanabe},
  title = {Constant temperature molecular dynamics calculation on Lennard-Jones
	fluid and its application to water},
  journal = {J. Chem.\ Phys.},
  year = {1983},
  volume = {78},
  pages = {2626--2634},
  number = {5},
  annote = {Establishes that only small range of friction coefficients (rather
	collision probabilities are allowed to preserve the dynamics)}
}

@ARTICLE{TANN83,
  author = {J. E. Tanner},
  title = {Intracellular Diffusion of Water},
  journal = {Arch.\ of Biochem.\ and Biophys.},
  year = {1983},
  volume = {224},
  pages = {416--428},
  number = {2}
}

@ARTICLE{TURR83,
  author = {N. J. Turro},
  title = {Influence of nuclear spin on chemical reactions: Magnetic isotope
	and magnetic field effects (A Review)},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {83},
  volume = {80},
  pages = {609--621}
}

@ARTICLE{Ulmn83,
  author = {K. Ulmner},
  title = {Protein Engineering},
  journal = SCI,
  year = {1983},
  volume = {219},
  pages = {666--671}
}

@ARTICLE{VARO83,
  author = { G.~V\'{a}r\'{o} and L. ~Keszthelyi},
  title = {Photoelectric signals from dried oriented purple membranes of {\em
	Halo\-bac\-terium halobium}},
  journal = BJ,
  year = {1983},
  volume = {43},
  pages = {47--51}
}

@ARTICLE{WAGN83,
  author = {Gerhard Wagner and Arthur Pardi and Kurt W\"uthrich},
  title = {Hydrogen Bond Length and $^1$H {NMR} Chemical Shifts in Proteins},
  journal = JACS,
  year = {1983},
  volume = {105},
  pages = {5948--5949}
}

@BOOK{AgGa82,
  title = {Electronic Excitation Energy Transfer in Condensed Matter},
  publisher = {North-Holland Publishing Company},
  year = {1982},
  author = {V. M. Agranovich and M. D. Galanin},
  address = {Amsterdam}
}

@ARTICLE{APIT82,
  author = {R. Apitz-Castro and M. K. Jain and G. H. de Haas},
  title = {Origin of the latency phase during the action of phospholipase {A}$_2$
	on unmodified phosphotidylcholine vesicles},
  journal = BBA,
  year = {1982},
  volume = {688},
  pages = {349--356}
}

@ARTICLE{BERK82,
  author = {Max Berkowitz and J. Andrew McCammon},
  title = {Molecular Dynamics with Stochastic Boundary Condition},
  journal = CPL,
  year = {1982},
  volume = {90},
  pages = {215--217},
  number = {3},
  annote = {THE reference for stochastic boundary; extended reaction region allows
	to use a vry simple bath model; value of friction determined from
	Einstein relation of diffusion constant; both, bath+reservoir are
	important to have},
  keywords = {reaction region; heat bath; reservoir region; liquid argon}
}

@ARTICLE{BIER82,
  author = {A. Bierzynski and P. S. Kim and R. L. Baldwin},
  title = {A Salt Bridge Stabilizes the Helix Formed by Isolated {C}-Peptide
	of {RN}ase~{A}},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA},
  year = {1982},
  volume = {79},
  pages = {2470--2474}
}

@ARTICLE{BOXE82,
  author = {S.G. Boxer and C.E.D. Chidsey and M.G. Roelofs},
  title = {Use of Large Magnetic Fields to Probe Photoinduced Electron-Transfer
	Reactions: An Example from Photosynthetic Reaction Centers},
  journal = {J.~Am.~Chem.~Soc.},
  year = {1982},
  volume = {104},
  pages = {1452--1454}
}

@ARTICLE{BRAI82,
  author = {M. Braiman and R. Mathies},
  title = {Resonance {Raman} Spectra of Bacteriorhodopsin's Primary Photoproduct:
	Evidence for a Distored 13-{\it cis} Retinal Chromophore},
  journal = PNAS,
  year = {1982},
  volume = {79},
  pages = {403--407}
}

@ARTICLE{BrBK82,
  author = {A. Br{\"u}nger and C. B. Brooks and M. Karplus},
  title = {Stochastic Boundary Conditions for Molecular Dynamics Simulations
	of {ST2} Water},
  journal = {Chem. Phys. Lett.},
  year = {1982},
  volume = {105},
  pages = {495--500}
}

@BOOK{BuAl82,
  title = {Molecular Mechanics},
  publisher = {America Chemical Society},
  year = {1982},
  author = {Ulrich Burkert and Norman Allinger},
  number = {117},
  series = {ACS Monography},
  nremark = {molecular mechanics, force field, review, introduction}
}

@ARTICLE{CiFR82,
  author = {G. Ciccotti and M. Ferrario and J.-P. Ryckaert},
  title = {Molecular Dynamics of Rigid Systems in Cartesian Coordinates: A General
	Formulation},
  journal = {Mol.\ Phys.},
  year = {1982},
  volume = {47},
  pages = {1253},
  number = {6}
}

@ARTICLE{EGEL82,
  author = {E. H. Egelman and N. Francis and D.~J. DeRosier},
  title = {F-actin is a helix with a random variable twist},
  journal = NAT,
  year = {1982},
  volume = {298},
  pages = {131--135}
}

@ARTICLE{Ferg82,
  author = {W. E. {Ferguson Jr.} and H. Flaschka and D. W. McLaughlin},
  title = {Nonlinear Normal Modes for the Toda Chain},
  journal = {J. Comput. Phys.},
  year = {1982},
  volume = {45},
  pages = {157--209}
}

@ARTICLE{DREW82,
  author = {A.~Fratini and M.~Lopka and H.~Drew and R.~Dickerson},
  title = {Reversible bending and helix geometry in a {B--DNA} Dodecamer {CGCGAATT--BR--CGCG}},
  journal = JBC,
  year = {1982},
  volume = {257}
}

@ARTICLE{GEOR82,
  author = {A. Georgallas and D.A. Pink},
  title = {Phase transition in monolayers of saturated lipids. Exact results
	and {M}onte {C}arlo simulations},
  journal = {J. Colloid. Interface Sci.},
  year = {1982},
  volume = {89},
  pages = {107}
}

@ARTICLE{VANG82,
  author = {R. van Grondelle and H.J.M. Kramer and C.P. Rijgersberg},
  title = {Energy transfer in the B800-B850-carotenoid light-harvesting complex
	of various mutants of {\em {R}hodopseudomonas sphaeroides} and of
	{\em {R}hodopseudomonas capsulata}},
  journal = {Biochim.~Biophys.~Acta},
  year = {1982},
  volume = {682},
  pages = {208--215}
}

@ARTICLE{GuBe82,
  author = {W.~F. van Gunsteren and H.~J.~C. Berendsen},
  title = {Algorithms for {B}rownian Dynamics},
  journal = {Mol.\ Phys.},
  year = {1982},
  volume = {45},
  pages = {637--647},
  number = {3}
}

@ARTICLE{GuKa82,
  author = {W. F. van Gunsteren and M. Karplus},
  title = {Effect of Constraints on the Dynamics of Macromolecules},
  journal = {Macromolecules},
  year = {1982},
  volume = {15},
  pages = {1528--1544},
  nremark = {a wealth of examples of tests},
  where = {TB lib}
}

@ARTICLE{HAUP82,
  author = {H. Hauptman},
  title = {On integrating the techniques of direct methods and isomorphous replacement.
	{I}. {T}he theoretical basis},
  journal = {Acta Cryst.},
  year = {1982},
  volume = {A38},
  pages = {289--294}
}

@BOOK{HAWT82,
  title = {Phospholipids},
  publisher = {Elsevier Science Publishing Company Inc.},
  year = {1982},
  author = {J. N. Hawthorne},
  address = {New York},
  edition = {1}
}

@INCOLLECTION{HUDS82,
  author = {Bruce S. Hudson and Bryan E. Kohler and Klaus Schulten},
  title = {Linear Polyene Electronic Structure and Potential Surfaces},
  booktitle = {Excited States},
  publisher = {Academic Press},
  year = {1982},
  editor = {Edward C. Lim},
  volume = {6},
  pages = {1--95},
  address = {New York}
}

@ARTICLE{JAIN82,
  author = {M.K. Jain and M.R. Egmond and H.M. Verheij and R.J. Apitz-Castro
	and R. Dijkman and G.H. de Haas},
  title = {Interaction of phospholipase {A$_2$} and phospholipid bilayers},
  journal = BBA,
  year = {1982},
  volume = {688},
  pages = {341--348}
}

@ARTICLE{JOHN82,
  author = {E. W. Johns},
  title = {The {HMG} chromosomal proteins},
  journal = {Academic Press, London},
  year = {1982}
}

@ARTICLE{JAHN82,
  author = {F. J{\"a}hnig and H. Vogel and L. Best},
  title = {Unifiying description of the effect of membrane proteins on lipid
	order. Verification for the melittin/dimyristoylphosphatidylcholine
	system},
  journal = BCH,
  year = {1982},
  volume = {27},
  pages = {6790}
}

@ARTICLE{KALI82,
  author = {O. Kalisky and M. Ottolenghi},
  title = {Branching Pathways in the Photocycle of Bacteriorhodopsin},
  journal = PCPB,
  year = {1982},
  volume = {35},
  pages = {109--115}
}

@ARTICLE{KYTE82b,
  author = {Kyte, J. and Doolittle, R. F.},
  title = {A Simple Method for Displaying the Hydropathic Character of a Protein},
  journal = {J. Mol. Biol.},
  year = {1982},
  volume = {157},
  pages = {105--132}
}

@ARTICLE{LIFS82,
  author = {S.~Lifson and P.~S.~Stern},
  title = {Born-Oppenheimer Energy Surfaces of Similar Molecules -- Interrelations
	Between Bond Lengths, Bond Angles, and Frequencies of Normal Vibrations
	in Alkanes},
  journal = JCP,
  year = {1982},
  volume = {77},
  pages = {4542--4550}
}

@ARTICLE{LIPA82,
  author = {Lipari, G. and Szabo, A.},
  title = {Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance
	Relaxation in Macromolecules},
  journal = JACS,
  year = {1982},
  volume = {104},
  pages = {4546--4559}
}

@ARTICLE{LOND82,
  author = {Erwin London and H. Gobind Khorana},
  title = {Denaturation and Renaturation of Bacteriohodopsin in Detergents and
	Lipid-Detergent Mixtures},
  journal = JBC,
  year = {1982},
  volume = {257},
  pages = {7003--7011}
}

@ARTICLE{MATZ82,
  author = {C. E. Matz and A. Jonas},
  title = {Micellar Complexes of Human Apolipoprotein {A-I} with Phosphatidylcholines
	and Cholesterol Prepared From Cholate-Lipid Dispersions},
  journal = JBC,
  year = {1982},
  volume = {257},
  pages = {4535--4540}
}

@BOOK{Mein82,
  title = {Models of Biological Pattern Formation},
  publisher = {Academic Press},
  year = {1982},
  author = {H. Meinhardt},
  address = {London}
}

@ARTICLE{MIER82,
  author = {S. Miertus and J. Tomasi},
  title = {Aproximate Evaluation of the Electrostatic Free Energy and Internal
	Energy Charges in Solution Processes.},
  journal = CP,
  year = {1982},
  volume = {65},
  pages = {239}
}

@ARTICLE{MILL82,
  author = {K.R. Miller},
  title = {Three-dimensional structure of a photosynthetic membrane},
  journal = NAT,
  year = {1982},
  volume = {300},
  pages = {53--55}
}

@ARTICLE{NORT82,
  author = {S. H. Northrup and M. R. Pear and C. Y. Lee and J. A. McCammon and
	M. Karplus},
  title = {Dynamical Theory of Activated Processes in Globular Proteins},
  journal = PNAS,
  year = {1982},
  volume = {79},
  pages = {4035--4039},
  annote = {june 1}
}

@ARTICLE{PABO82,
  author = {C.~O.~Pabo and W.~Krovatin and A.~Jeffrey and R.~T.~Sauer},
  title = {The {N}-Terminal Arms of Lambda Repressor Wrap Around the Operator~{DNA}},
  journal = NAT,
  year = {1982},
  volume = {298},
  pages = {441--443}
}

@ARTICLE{PLOE82,
  author = {P. van der Ploeg and H. J. C. Berendsen},
  title = {Molecular Dynamics Simulation of a Bilayer Membrane},
  journal = JCP,
  year = {1982},
  volume = {76},
  pages = {3271--3276},
  number = {6},
  annote = {challenges kink-model; 2x16 decanoate molecules; periodic boundary
	in 2D; SHAKE for bond length; 80ps simulation; dt=8fs; T=300K; cooperative
	tilt; S$_{\rm CD}=2/3 {\rm S}_{\rm xx}+1/3 {\rm S}_{\rm yy}$; investigation
	of anisotropic rotation},
  keywords = {order parameter; tilt; local tilt; chain tilt;distribution functions},
  suggestions = {investigate anisotropic rotation}
}

@INCOLLECTION{SCHU82,
  author = {Klaus Schulten},
  title = {Magnetic Field Effects in Chemistry and Biology},
  booktitle = {Fest\-k\"orper\-probleme},
  publisher = {Vieweg},
  year = {1982},
  editor = {J. Treusch},
  volume = {22},
  pages = {61--83},
  address = {Braunschweig}
}

@ARTICLE{SEN82,
  author = {R. Sen and J. Carriker and V. Balogh-Nair and K. Nakanishi},
  title = {Studies of a Photoaffinity Label for Bovine Rhodopsin},
  journal = JACS,
  year = {1982},
  volume = {104},
  pages = {3214--3216}
}

@ARTICLE{SKAR82,
  author = {Robert Skarjune and Eric Oldfield},
  title = {Physical Studies of Cell Surface and Cell Membrane Structure. Deuterium
	Nuclear Magnetic Resonance Studies of $N$--Palmitoylglucosylceramide
	(Cerebroside) Head Group Structure},
  journal = BCH,
  year = {1982},
  volume = {21},
  pages = {3154--3160}
}

@INCOLLECTION{SLOT82,
  author = {A. J. Slotboom and H. M. Verheij and G. H. de Haas},
  title = {On the mechanism of phospholipase {A}$_2$},
  booktitle = {Phospholipids},
  publisher = {Elsevier Biomedical Press},
  year = {1982},
  editor = {J. N. Hawthorne and G. B. Ansell},
  pages = {359--435},
  address = {New York}
}

@INPROCEEDINGS{STAU82,
  author = {Dietrich Stauffer and Antonio Coniglio and Mireille Adam},
  title = {Gelation and Critical Phenomena},
  booktitle = {Polymer Networks},
  year = {1982},
  volume = {44},
  series = {Advances in Polymer Science},
  pages = {103--158}
}

@ARTICLE{SWIN82,
  author = {N. V. Swindale},
  title = {A Model for the Formation of Orientation Columns},
  year = {1982},
  volume = {215},
  pages = {211--230},
  jounal = {Proc. R. Soc. Lond. B}
}

@ARTICLE{SABW82,
  author = {W.C. Swope and H.C. Andersen and P.H. Berens and K.R. Wilson},
  title = {A computer simulation method for the calculation of equilibrium constants
	for the formation of physical clusters of molecules: application
	to small water clusters},
  journal = {J. Chem.\ Phys.},
  year = {1982},
  volume = {76},
  pages = {637--649}
}

@BOOK{SZAB82,
  title = {Modern quantum chemistry: Introduction to advanced electronic structure
	theory},
  publisher = {MacMillan},
  year = {1982},
  author = {A. Szabo and N.S. Ostlund},
  address = {New York}
}

@ARTICLE{TeEi82,
  author = {T. C. Terwilliger and D. Eisenberg},
  title = {The structure of Melittin},
  journal = {J. Biol. Chem.},
  year = {1982},
  volume = {257},
  pages = {6010}
}

@ARTICLE{THUL82,
  author = {Keith R. Thulborn and John C. Waterton and Paul M. Matthews and George
	K. Radda},
  title = {Oxygenation Dependence of the Transverse Relaxation Time of Water
	Protons in Whole Blood at High Field},
  journal = {Biochimica et Biophysica Acta},
  year = {1982},
  volume = {714},
  pages = {265--270},
  brief = {Increase in T2 rate with increasing blodd deox. arises from diffusion
	of water through susceptabliity-induced field gradients},
  keywords = {paramagnetic}
}

@ARTICLE{WARS82,
  author = {A.~Warshel and N.~Barboy},
  title = {Energy Storage and Reaction Pathways in the First Step of the Vision
	Process},
  journal = JACS,
  year = {1982},
  volume = {104},
  pages = {1469--1476}
}

@ARTICLE{WARW82,
  author = {J.\ Warwicker and H.\ C.\ Watson},
  title = {Calculation of the Electric Potential in the Active Site Cleft due
	to $\alpha$-Helix Dipoles},
  journal = JMB,
  year = {1982},
  volume = {157},
  pages = {671--679}
}

@ARTICLE{WINT82,
  author = {J.M. de Winter and G.M. Vianen and H. van den Bosch},
  title = {Purification of rat liver mitochondrial phospholipase {A$_2$}},
  journal = BBA,
  year = {1982},
  volume = {712},
  pages = {332--341},
  annote = {intracellular PLA2}
}

@ARTICLE{Wisd82,
  author = {J. Wisdom},
  title = {The Origin of the {K}irkwood Gaps: {A} Mapping for Asteroidal Motion
	near the 3/1 Commensurability},
  journal = {Astr.\ J.},
  year = {1982},
  volume = {87},
  pages = {577--593},
  nremark = { Wisdom: first use of delta function formulation}
}

@TECHREPORT{MALS81,
  author = {C. {von der Malsburg}},
  title = {The correlation Theory of Brain Function},
  institution = {Department of Neurobiology, Max Planck Institute for Biophysical
	Chemistry},
  year = {1981},
  type = {Internal Report},
  number = {81--2},
  address = {G\"ottingen, FRG}
}

@ARTICLE{ASHC81,
  author = {R.G. Ashcroft and H.G.L. Coster and J.R. Smith},
  title = {The molecular organisation of biomolecular lipid membranes. The dielectric
	structure of the hydrophilic/hydrophobic interface},
  journal = BBA,
  year = {1981},
  volume = {643},
  pages = {191--204}
}

@ARTICLE{BAYL81,
  author = {Hagan Bayley and Kuo-Sen Huang and Ramachandran Radhakrishnan and
	Alonzo H. Ross and Yohtaroh Takagaki and H. Gobind Khorana},
  title = {Site of Attachment of Retinal in Bacteriorhodopsin},
  journal = PNAS,
  year = {1981},
  volume = {78},
  pages = {2225--2229}
}

@ARTICLE{BECK81,
  author = {W. Beck and W. Wiltschko},
  title = {Trauerschn\"apper ({\em Ficedula hypoleuca} Pallas) orientieren sich
	nicht-visuell mit Hilfe des Magnetfeldes},
  journal = {Vogelwarte},
  year = {1981},
  volume = {31},
  pages = {168--174}
}

@BOOK{BRON81,
  title = {Taschenbuch der Mathematik},
  publisher = {Harry Deutsch},
  year = {1981},
  author = {Bronstein and Semendjajew},
  address = {Thun, Frankfurt/Main},
  edition = {21},
  annote = {t-test (Student Verteilung) on page 725}
}

@ARTICLE{CEDE81,
  author = {L. S. Cederbaum and H.~K{\"o}ppel and W. Domcke},
  title = {Multimode Vibronic Coupling Effects in Molecules},
  journal = IJQCS,
  year = {1981},
  volume = {15},
  pages = {251--267}
}

@ARTICLE{CEVC81,
  author = {G. Cevc and A. Watts and D. Marsh},
  title = {Titration of the phase transition of phosphatidylserine bilayer membranes.
	Effects of p{H}, surface electrostatics, ion binding and head-group
	hydration},
  journal = BCH,
  year = {1981},
  volume = {20},
  pages = {4955--4965}
}

@ARTICLE{ChSh81a,
  author = {M. M. Chawla and S. R. Sharma},
  title = {Intervals of periodicity and absolute stability of explicit Nystr\"om
	methods for $y''=f(x,y)$},
  journal = {BIT},
  year = {1981},
  volume = {21},
  pages = {455--464}
}

@ARTICLE{ChSh81b,
  author = {M. M. Chawla and S. R. Sharma},
  title = {Families of fifth order Nystr\"om methods for $y''=f(x,y)$ and intervals
	of perodicity},
  journal = {computing},
  year = {1981},
  volume = {26},
  pages = {247--256}
}

@ARTICLE{COGD81,
  author = {R.J. Cogdell and M. F. Hipkins and W. MacDonald and T.G. Truscott},
  title = {Energy tranfer between the carotenoid and the bacteriochlorophyll
	within the B800-850 light-harvesting pigment-protein complex of {\em
	Rhodopseudomonas acidophila}},
  journal = BBA,
  year = {1981},
  volume = {634},
  pages = {191--202}
}

@ARTICLE{DENN81,
  author = {E. A. Dennis and P. L. Darke and R. A. Deems and C. R. Kensil and
	A. Pluckthun},
  title = {Cobra venom phospholipase {A$_2$}: a review of its action toward
	lipid/water interfaces},
  journal = {Mol. Cell. Biochem.},
  year = {1981},
  volume = {36},
  pages = {37--45}
}

@ARTICLE{DICK81,
  author = {R.~E.~Dickerson and H.~R.~Drew.},
  title = {Structure of a {B-DNA} dodecamer. {II}. Influence of base sequence
	on helix structure},
  journal = JMB,
  year = {1981},
  volume = {149},
  pages = {761--786}
}

@ARTICLE{DIJK81a,
  author = {B. W. Dijkstra and J. Drenth and K. H. Kalk},
  title = {The Active Site and the Catalytic Mechanism of Phospholipase~{A}$_2$},
  journal = NAT,
  year = {1981},
  volume = {289},
  pages = {604--606},
  annote = {classical bovine PLA2 structure, get it!}
}

@ARTICLE{DIJK81b,
  author = {B. W. Dijkstra and K. H. Kalk and W. G. J. Hol and J. Drenth},
  title = {Structure of Bovine Pancreatic Phospholipase {A}$_2$ at 1.7\,{\AA\
	} Resolution},
  journal = JMB,
  year = {1981},
  volume = {147},
  pages = {93--123},
  annote = {get it! original paper for bovine pla structure}
}

@ARTICLE{DOUK81,
  author = {A. Doukas and A. Pandi and T. Suzuki and R. Callender and M. Ottolenghi},
  title = {On the Mechanism of Hydrogen-Deuterium Exchange in Bacteriorhodopsin},
  journal = BJ,
  year = {1981},
  volume = {33},
  pages = {275--280}
}

@ARTICLE{DREW81A,
  author = {H.~R.~Drew and R.~E.~Dickerson.},
  title = {Structure of a {B-DNA} dodecamer. {III}. Geometry of hydration},
  journal = JMB,
  year = {1981},
  volume = {151},
  pages = {535--556}
}

@ARTICLE{DREW81,
  author = {H.~R.~Drew and R.~M.~Wing and T.~Takano and C.~Broka and S.~Tanaka
	and K.~Itikura and R.~E.~Dickerson.},
  title = {Structure of a {B-DNA} dodecamer. {I}. Conformation and dynamics},
  journal = PNAS,
  year = {1981},
  volume = {78},
  pages = {2179--2983}
}

@ARTICLE{ESTE81,
  author = {James E. Estes and Lynn A. Selden and Lewis C. Gershman},
  title = {Mechanism of Action of Phalloidin on the Polymerization of Muscle
	Actin},
  journal = BCH,
  year = {1981},
  volume = {20},
  pages = {708--712}
}

@ARTICLE{FELS81,
  author = {J. Felsenstein},
  title = {Evolutionary trees from {DNA} sequences: A maximum likelihood approach},
  journal = {J. Mol. Evol.},
  year = {1981},
  volume = {17},
  pages = {368--376}
}

@ARTICLE{FITE81,
  author = {K.V. Fite and M. Brecha and H.J. Karten and S.P. Hunt},
  title = {Displaced ganglion cells and the accessory optic system of pigeons},
  journal = {J.~Comp.~Neurol.~},
  year = {1981},
  volume = {195},
  pages = {279--288}
}

@BOOK{GOLD81,
  title = {{K}lassische {M}echanik},
  publisher = {Akademische Verlagsgesellschaft},
  year = {1981},
  author = {Herbert Goldstein},
  address = {Wiesbaden}
}

@ARTICLE{GRES81,
  author = {G. S. Grest and S. R. Nagel and A. Rahman and Witten, Jr., T. W.},
  title = {Density of States and the Velocity Autocorrelation Function Derived
	from Quench Studies},
  journal = JCP,
  year = {1981},
  volume = {74},
  pages = {3532--3534},
  number = {6}
}

@ARTICLE{VANG81,
  author = {W. F. van Gunsteren and J.C. Berendsen and J. A. C. Rullmann},
  title = {Stochastic Dynamics for molecules with constraints. Brownian dynamics
	of $n$-alkanes},
  journal = MP,
  year = {1981},
  volume = {44},
  pages = {69--95}
}

@ARTICLE{HAUS81,
  author = {H. Hauser and I. Pascher and R. H. Pearson and S. Sundell},
  title = {Preferred conformation and molecular packing of phatidylethanolamine
	and phosphatidylcholine},
  journal = BBA,
  year = {1981},
  volume = {650},
  pages = {21--51},
  annote = {requested Tx=19920908.}
}

@ARTICLE{HENE81,
  author = {G. Heney and G. A. Orr},
  title = {The purification of avidin and its derivatives on 2-immunobiotin-6-aminohexylsepharose
	4B},
  journal = {Anal. Biochem.},
  year = {1981},
  volume = {114},
  pages = {92--96},
  annote = {june 1}
}

@ARTICLE{Heye81,
  author = {D. M. Heyes},
  title = {Electrostatic potentials and fields in infinite point charge lattices},
  journal = {J. Chem. Phys.},
  year = {1981},
  volume = {74},
  pages = {1924}
}

@BOOK{HoEa81,
  title = {Computer Simulation Using Particles},
  publisher = {McGraw-Hill},
  year = {1981},
  author = {R.~W. Hockney and J.~W. Eastwood},
  address = {New York}
}

@ARTICLE{HOFF81,
  author = {A.J. Hoff},
  title = {Magnetic field effects on photosynthetic reactions},
  journal = {Quart.~Rev.~Biophys.},
  year = {1981},
  volume = {14},
  pages = {599--665}
}

@ARTICLE{HUAN81,
  author = {Kuo-Sen Huang and Hagan Bayley and Mei-June Liao and Erwin London
	and H. Gobind Khorana},
  title = {Refolding of an Integral Membrane Protein},
  journal = JBC,
  year = {1981},
  volume = {256},
  pages = {3802--3809}
}

@ARTICLE{HUNT81,
  author = {Katherine L. C. Hunt and John Ross},
  title = {Path integral solutions of stochastic equations for nonlinear irreversible
	processes: The uniqueness of the thermodynamic {Lagrangian}},
  journal = JCP,
  year = {1981},
  volume = {75},
  pages = {976--984},
  number = {2}
}

@ARTICLE{IWAS81,
  author = {T. Iwasa and F. Tokunaga and T. Yoshizawa},
  title = {Photochemical Reaction of 13-{\it cis}-Bacteriorhodopsin Studied
	by Low Temperature Spectrophotometry},
  journal = PCPB,
  year = {1981},
  volume = {33},
  pages = {539--545}
}

@ARTICLE{JACO81,
  author = {R. E. Jacobs and E. Oldfield},
  title = {{NMR} of membranes},
  journal = {Progr. {NMR} Spectroscopy},
  year = {1981},
  volume = {14},
  pages = {113--136}
}

@ARTICLE{JORG81,
  author = {W.L. Jorgensen},
  title = {Transferable intermolecular potential functions for water, alcohol,
	and esters. Application to liquid water},
  journal = JACS,
  year = {1981},
  volume = {103},
  pages = {335--340}
}

@ARTICLE{JAHN81a,
  author = {F. J{\"a}hnig},
  title = {Critical effects from lipid--protein interaction in membranes I.
	Theoretical description},
  journal = BJ,
  year = {1981},
  volume = {36},
  pages = {329}
}

@ARTICLE{JAHN81b,
  author = {F. J{\"a}hnig},
  title = {Critical effects from lipid--protein interaction in membranes II.
	Interpretation of experimental results},
  journal = BJ,
  year = {1981},
  volume = {36},
  pages = {347}
}

@ARTICLE{KALI81,
  author = {O. Kalisky and M. Ottolenghi and B. Honig and R. Korenstein},
  title = {Environmental Effects on Formation and Photoreaction of the {M}412
	Photoproduct of Bacteriorhodopsin: Implications for the Mechanism
	of Proton Pumping},
  journal = BCH,
  year = {1981},
  volume = {20},
  pages = {649--655}
}

@BOOK{KAMP81,
  title = {Stochastic Processes in Physics and Chemistry},
  publisher = {North-Holland},
  year = {1981},
  author = {N. G. van Kampen},
  address = {Amsterdam, New York}
}

@ARTICLE{KENN90,
  author = {D.F. Kennedy and A.J. Slotboom and G.H. de Haas and D. Chapman},
  title = {A {F}ourier Transform infrared spectrospic ({FTIR}) study of porcine
	and bovine pancreatic phospholipase {A$_2$} and their interaction
	with substrate analogues and a transition-state inhibitor},
  journal = BBA,
  year = {1981},
  volume = {1040},
  pages = {317--326}
}

@ARTICLE{KIRS81A,
  author = {J.L. Kirschvink},
  title = {The horizontal magnetic dance of honeybees is compatible with a single-domain
	ferromagnetic magnetoreceptor},
  journal = {BioSystems},
  year = {1981},
  volume = {14},
  pages = {193--203}
}

@ARTICLE{KIRS81,
  author = {J.L. Kirschvink and J.L. Gould},
  title = {Biogenic magnetite as a basis for magnetic field detection in animals},
  journal = {BioSystems},
  year = {1981},
  volume = {13},
  pages = {181--201}
}

@ARTICLE{LAMM81,
  author = {Gene Lamm and Klaus Schulten},
  title = {Extended {B}rownian Dynamics Approach to Diffusion-Controlled Processes},
  journal = JCP,
  year = {1981},
  volume = {75},
  pages = {365--371}
}

@ARTICLE{LARS81,
  author = {S.~Larsson},
  title = {Electron Transfer in Chemical and Biological Systems. Orbital Rules
	for Nonadiabatic Transfer.},
  journal = JACS,
  year = {1981},
  volume = {103},
  pages = {4034--4040}
}

@ARTICLE{LaWe81,
  author = {S.~S. Lavenberg and P.~D. Welch},
  title = {A Perspective on the Use of Control Variables to Increase the Efficiency
	of {M}onte {C}arlo Simulations},
  journal = {Management Science},
  year = {1981},
  volume = {27},
  pages = {322--335}
}

@ARTICLE{MCCA81,
  author = {Darrel R. McCaslin and Charles Tanford},
  title = {Effects of Detergent Micelles on the Recombination Reaction of Opsin
	and 11-{\it cis}-Retinal},
  journal = BCH,
  year = {1981},
  volume = {20},
  pages = {5207--5212},
  annote = {Basic stuff about retinal and micelles}
}

@ARTICLE{MIER81,
  author = {S. Miertus and E. Scrocco and J. Tomasi},
  title = {Electrostatic Interaction of a Solute with a Continium. A Direct
	Utilization of ab initio Molecular Potentials for the Prevision of
	Solvent Effects.},
  journal = CP,
  year = {1981},
  volume = {55},
  pages = {117}
}

@ARTICLE{NAGE81,
  author = {S. R. Nagel and A. Rahman and G. S. Grest},
  title = {Normal-Mode Analysis by Quench-Echo Techniques: Localization in a
	Amorphous Solid},
  journal = PRL,
  year = {1981},
  volume = {47},
  pages = {1665--1668},
  number = {23}
}

@ARTICLE{NAGL81,
  author = {J. F. Nagle and M. Mille},
  title = {Molecular-Models of Proton Pumps},
  journal = JCP,
  year = {1981},
  volume = {74},
  pages = {1367--1372}
}

@ARTICLE{PETE81,
  author = {Reiner Peters and Axel Br{\"u}nger and Klaus Schulten},
  title = {Continuous Fluorescence Microphotolysis: A Sensitive Method for Study
	of Diffusion Processes in Single Cells},
  journal = PNAS,
  year = {1981},
  volume = {78},
  pages = {962--966}
}

@BOOK{Rans81,
  title = {Computers and Embryos: Models in Developmental Biology},
  publisher = {John Wiley},
  year = {1981},
  author = {Robert Ransom},
  address = {New York}
}

@ARTICLE{SCHU81,
  author = {Klaus Schulten and Zan Schulten and Attila Szabo},
  title = {Dynamics of Reactions Involving Diffusive Barrier Crossing},
  journal = JCP,
  year = {1981},
  volume = {74},
  pages = {4426--4432}
}

@ARTICLE{TOWN81,
  author = {Paul Towner and Wolfgang Gaertner and Baerbel Walckhoff and Dieter
	Osterhelt and Henning Hopf},
  title = {Regeneration of Rhodopsin and Bacteriorhodopsin: {T}he Role of Retinal
	Analogues as Inhibitors},
  journal = EJB,
  year = {1981},
  volume = {117},
  pages = {353--359}
}

@ARTICLE{VERH81,
  author = {H. M. Verheij and A. J. Slotboom and G. H. de Haas},
  title = {Structure and function of phospholipase {A}$_2$},
  journal = {Rev. Physiol. Biochem. Pharmacol.},
  year = {1981},
  volume = {91},
  pages = {91--203}
}

@ARTICLE{WeKo81,
  author = {P. K. Weiner and P. A. Kollman},
  title = {{AMBER}: Assisted Model Building with Energy Refinement. {A} General
	Program for Modeling Molecules and Their Interactions},
  journal = JCC,
  year = {1981},
  volume = {2},
  pages = {287--303}
}

@ARTICLE{WILT81,
  author = {W. Wiltschko and R. Wiltschko},
  title = {Disorientation of inexperienced young pigeons after transportation
	in total darkness},
  journal = NAT,
  year = {1981},
  volume = {291},
  pages = {433--434}
}

@ARTICLE{ALLE80,
  author = {J.C.~Allegra and M.E.~Lippman and E.B.~Thompson and R.~Simon and
	A.~Barlock and K.K.~Huff and H.M.~Do and S.C.~Aitkin and R.~Warren.},
  title = {Estrogen receptor status: an important variable in predicting response
	to endocrine therapy in metastatic breast cancer},
  journal = {European Journal Cancer},
  year = {1980},
  volume = {16},
  pages = {323--331}
}

@ARTICLE{Ande80,
  author = {H.~C. Andersen},
  title = {Molecular Dynamics Simulations at Constant Pressure and/or Temperature},
  journal = {J. Chem.\ Phys.},
  year = {1980},
  volume = {72},
  pages = {2384--2393}
}

@ARTICLE{ATON80,
  author = {B. Aton and A. G. Doukas and D. Narva and R. Callender and U. Dinur},
  title = {Resonance {Raman} Studies of the Primary Photo-Chemical Event in
	Visual Pigments},
  journal = BJ,
  year = {1980},
  volume = {29},
  pages = {79--84}
}

@ARTICLE{BAYE80,
  author = {E. A. Bayer and M. Wilcheck},
  title = {The use of avidin-biotin complex as a tool in molecular biology},
  journal = {Methods Biochem. Anal.},
  year = {1980},
  volume = {26},
  pages = {1--45},
  annote = {june 1}
}

@ARTICLE{BENN80,
  author = {W. S. Bennett and T. A. Steitz},
  title = {Structure of a complex between yeast hexokinase {A} and glucose {I}.},
  journal = JMB,
  year = {1980},
  volume = {140},
  pages = {183--209}
}

@ARTICLE{BENN80A,
  author = {W. S. Bennett and T. A. Steitz},
  title = {Structure of a complex between yeast hexokinase {A} and glucose {II}.},
  journal = JMB,
  year = {1980},
  volume = {140},
  pages = {211--230}
}

@BOOK{BOON80,
  title = {Molecular Hydrodynamics},
  publisher = {Dover Publications, Inc},
  year = {1980},
  author = {J. P. Boon and S. Yip},
  address = {New York}
}

@BOOK{CANT80,
  title = {Biophysical Chemistry},
  publisher = {W. H. Freeman and Company},
  year = {1980},
  author = {C. R. Cantor and P. R. Schimmel},
  volume = {II},
  address = {New York}
}

@BOOK{CANT80A,
  title = {Biophysical Chemistry},
  publisher = {W. H. Freeman and Company},
  year = {1980},
  author = {C. R. Cantor and P. R. Schimmel},
  volume = {I},
  address = {New York}
}

@BOOK{CANT80B,
  title = {Biophysical Chemistry},
  publisher = {W. H. Freeman and Company},
  year = {1980},
  author = {C. R. Cantor and P. R. Schimmel},
  volume = {III},
  address = {New York}
}

@INCOLLECTION{CLEM80,
  author = {E. Clementi},
  title = {Computational Aspects for Large Chemical Systems},
  booktitle = {Lecture Notes in Chemistry},
  publisher = {Springer},
  year = {1980},
  address = {New York}
}

@ARTICLE{DINU80,
  author = {Uri Dinur and Barry Honig and Klaus Schulten},
  title = {On the Nature of Excited Electronic States in Cyanine Dyes: Implications
	for Visual Pigment Spectra},
  journal = CPL,
  year = {1980},
  volume = {72},
  pages = {493--497},
  number = {3},
  annote = {jun 15}
}

@ARTICLE{DIRK80,
  author = {G. Dirks and A. L. Moore and T. A. Moore and D. Gust},
  title = {Light Absorption and Energy Transfer in Polyene-Porphyrin Esters},
  journal = PCPB,
  year = {1980},
  volume = {32},
  pages = {277--280}
}

@ARTICLE{DUPU80,
  author = {P. Dupuis and F. Harosi and C. Sandorfy and J. M. Leclercq and D.
	Vocelle},
  title = {1st Step in Vision\ --\ Proton-Transfer or Isomerization},
  journal = RCB,
  year = {1980},
  volume = {39},
  pages = {247--258}
}

@ARTICLE{EISE80b,
  author = {E. Eisenberg and T. L. Hill and Y. D. Chen},
  title = {Cross-bridge Model of Muscle Contraction},
  journal = BJ,
  year = {1980},
  volume = {29},
  pages = {2195}
}

@ARTICLE{FRIE80,
  author = {C. Frieden and D. Lieberman and H. R. Gilbert},
  title = {A Flourescent Prope for Conformational Changes in Skeletal Muscle
	{G}-Actin},
  journal = JBC,
  year = {1980},
  volume = {255},
  pages = {8991--8993}
}

@BOOK{Gold80,
  title = {Classical mechanics},
  publisher = {Addison-Wesley},
  year = {1980},
  author = {H. Goldstein},
  address = {Reading, Massachusetts}
}

@ARTICLE{GRES80,
  author = {G. S. Grest and S. R. Nagel and A. Rahman},
  title = {Quench Echoes in Molecular Dynamics --- A New Phonon Spectroscopy},
  journal = SSC,
  year = {1980},
  volume = {36},
  pages = {875--879}
}

@ARTICLE{HAUS80,
  author = {H. Hauser and I. Pascher and S. Sundell},
  title = {Conformation of phospholipids. Crystal structure of a lysophosphatidylcholine
	analogue},
  journal = JMB,
  year = {1980},
  volume = {137},
  pages = {249},
  annote = {requested Tx=19921018.; X-ray structure of LPPC, which is the product
	of Phospholipase {A$_2$} activity},
  keywords = {Phospholipase {A$_2$}}
}

@BOOK{HiJo80,
  title = {Development of the vertebrate limb: an approach through experiment,
	genetics and evolution},
  publisher = {Oxford University Press},
  year = {1980},
  author = {J. R. Hinchliffe and D. R. Johnson},
  address = {New York}
}

@ARTICLE{JOST80,
  author = {P.C. Jost and O.H. Griffith},
  title = {The lipid--protein interface in biological membranes},
  journal = {Ann. N.Y. Acad. Sci.},
  year = {1980}
}

@ARTICLE{KARP80,
  author = {Martin Karplus and Peter Rossky},
  title = {Solvation: A Molecular Dynamics Study of a Dipeptide in Water},
  journal = {ACS Symposium Series},
  year = {1980},
  volume = {127},
  pages = {23--42}
}

@ARTICLE{KESZ80,
  author = {L.~Keszthelyi and P.~Ormos},
  title = {Electrical signals associated with the photocycle of bacteriorhodopsin},
  journal = FEBS,
  year = {1980},
  volume = {109},
  pages = {189--193}
}

@ARTICLE{KLUG80,
  author = {A.~Klug and D.~Rhodes},
  title = {Helical periodicity of {DNA} determined by enzyme digestion},
  journal = NAT,
  year = {1980},
  volume = {286},
  pages = {573--578},
  annote = {original ref to fact that {DNA}in solution has 10.3 to 10.6 bp/turn
	10/bp turn in xstals is below}
}

@ARTICLE{KNAP80,
  author = {Ernst-Walter Knapp and Klaus Schulten and Zan Schulten},
  title = {Proton Conduction in Linear Hydrogen-Bonded Systems},
  journal = CP,
  year = {1980},
  volume = {46},
  pages = {215--229}
}

@ARTICLE{KNOW80,
  author = {J.R. Knowles},
  title = {Enzyme-catalyzed phosphoryl transfer reactions},
  journal = ARB,
  year = {1980},
  volume = {49},
  pages = {877--919}
}

@ARTICLE{LePS80a,
  author = {S. W. de Leeuw and J. W. Perram and E. R. Smith},
  title = {Simulation of Electrostatic Systems in Periodic Boundary Conditions.
	{I}. {L}attice Sums and Dielectric Constants},
  journal = {Proc.\ R. Soc.\ Lond. A},
  year = {1980},
  volume = {373},
  pages = {27--56}
}

@ARTICLE{LePS80b,
  author = {S. W. de Leeuw and J. W. Perram and E. R. Smith},
  title = {Simulation of Electrostatic Systems in Periodic Boundary Conditions.
	II. Equivalence of boundary donditions},
  journal = {Proc.\ R. Soc.\ Lond. A},
  year = {1980},
  volume = {373},
  pages = {56--66}
}

@ARTICLE{LePS80c,
  author = {S. W. de Leeuw and J. W. Perram and E. R. Smith},
  title = {Simulation of Electrostatic Systems in Periodic Boundary Conditions.
	II. Further theory and applications},
  journal = {Proc.\ R. Soc.\ Lond. A},
  year = {1980},
  volume = {378},
  pages = {177--193}
}

@ARTICLE{LELK80,
  author = {P.I. Lelkes and I.R. Miller},
  title = {Perturbations of Membrane structure by optical probes: 1. Location
	and structural sensitivity of merocyanine 540 bound to phospholipid
	membranes},
  journal = {J. Membrane Biol},
  year = {1980},
  volume = {52},
  pages = {1--15}
}

@ARTICLE{LENG80,
  author = {B. Lengsfield},
  title = {General Second Order MCSCF Theory: A Density Matrix Directed Algorithm.},
  journal = JCP,
  year = {1980},
  volume = {73},
  pages = {382}
}

@ARTICLE{MAAS80,
  author = {H.~Maass and W.~Jonat and G.~Stolzenbach and G.~Trams},
  title = {The problem of nonresponding estrogen--receptor positive patients
	with advanced breast cancer},
  journal = {Cancer (Phila.)},
  year = {1980},
  volume = {6},
  pages = {2835--2837}
}

@ARTICLE{MCGH80,
  author = {J. D. {McGhee} and G. Felsenfeld},
  title = {Nucleosome structure},
  journal = ARB,
  year = {1980},
  volume = {49},
  pages = {1115--56}
}

@ARTICLE{NAKA80,
  author = {K. Nakanishi and M. Arnaboldi and V. Baloghnair and B. Honig},
  title = {An External Point-Charge Model for Bacteriorhodopsin to Account for
	Its Purple Color},
  journal = JACS,
  year = {1980},
  volume = {102},
  pages = {7945--7947}
}

@ARTICLE{NAQV80,
  author = {K. R. Naqvi},
  title = {The Mechanism of Singlet-Singlet Excitation Energy Transfer from
	Carotenoids to Chlorophyll},
  journal = PCPB,
  year = {1980},
  volume = {31},
  pages = {523--524}
}

@ARTICLE{PRAT80,
  author = {L. R. Pratt and D. Chandler},
  title = {Effects of solute0solvent attractive forces on hydrophobic correlations},
  journal = JCP,
  year = {1980},
  volume = {73},
  pages = {3434--3441},
  number = {7},
  annote = {june 1}
}

@ARTICLE{ROOS80,
  author = {B. Roos and P. Taylor and P. Siegbahn},
  title = {A Complete Active Space SCF Method (CASSCF) Using a Density Matrix
	Fprmulated Super-CI Approach.},
  journal = CP,
  year = {1980},
  volume = {48},
  pages = {157}
}

@ARTICLE{SCHU80A,
  author = {Klaus Schulten and Uri Dinur and Barry Honig},
  title = {The Spectra of Carbonium Ions, Cyanine Dyes, and Protonated {Schiff}
	Base Polyenes},
  journal = JCP,
  year = {1980},
  volume = {73},
  pages = {3927--3935},
  number = {8},
  annote = {15 Oct}
}

@ARTICLE{SCHU80,
  author = {Klaus Schulten and Zan Schulten and Attila Szabo},
  title = {Reactions Governed by a Binomial Redistribution Process. {T}he {E}hrenfest
	Urn Problem},
  journal = PHY,
  year = {1980},
  volume = {100A},
  pages = {599--614}
}

@ARTICLE{SEEL80,
  author = {J. Seelig and A. Seelig},
  title = {Lipid conformation in model membranes and biological membranes},
  journal = {Quarterly Review of Biophysics},
  year = {1980},
  volume = {13},
  pages = {19--61}
}

@ARTICLE{SEEL80b,
  author = {J. Seelig and A. Seelig},
  title = {Lipid conformation in model membranes and biological membranes},
  journal = {Q. Rev. Biophys.},
  year = {1980},
  volume = {13},
  pages = {19--61}
}

@ARTICLE{SEEL80a,
  author = {J. Seelig and L. Tamm and S. Fleischer and L. Hymel},
  title = {Deuterium and phosphorous {NMR} and fluorecence depolarization studies
	of functional reconstituted sarcoplasmic reticulum membrane vesicles},
  year = {1980}
}

@ARTICLE{SHIO80,
  author = {J.A. Shiozawa and P.A. Cuendet and G. Drews and H. Zuber},
  title = {Isolation and characterization of the polypeptide components from
	light-harvesting pigment-protein complex {B}800--850 of {{\it {R}hodopseudomonas
	capsulata\/}}},
  journal = {European Journal of Biochemistry},
  year = {1980},
  volume = {111},
  pages = {455--60}
}

@ARTICLE{SZAB80,
  author = {Attila Szabo and Klaus Schulten and Zan Schulten},
  title = {First Passage Time Approach to Diffusion Controlled Reactions},
  journal = JCP,
  year = {1980},
  volume = {72},
  pages = {4350--4357}
}

@ARTICLE{TAVA80,
  author = {Paul Tavan and Klaus Schulten},
  title = {An Efficient Approach to {CI}: General Matrix Element Formulas for
	Spin-Coupled Particle-Hole Excitations},
  journal = JCP,
  year = {1980},
  volume = {72},
  pages = {3547--3576},
  number = {6},
  annote = {MAR 15}
}

@ARTICLE{TSUD80,
  author = {M. Tsuda and M. Glaccum and B. Nelson and T. G. Ebrey},
  title = {Light Isomerizes the Chromophore of Bacteriorhodopsin},
  journal = NAT,
  year = {1980},
  volume = {287},
  pages = {351--353}
}

@ARTICLE{VERH80,
  author = {H. M. Verheij and J. J. Volwerk and E. H. Jansen and W. C. Puyk and
	B. W. Dijkstra and J. Drenth and G. H. de Haas},
  title = {Methylation of Histidine-48 in pancreatic phospholipase {A}$_2$.
	Role of histidine and calcium ion in the catalytic mechanism},
  journal = BCH,
  year = {1980},
  volume = {19},
  pages = {743},
  annote = {get it!}
}

@ARTICLE{WaCo80,
  author = {Y.~Wallach and V.~Conrad},
  title = {On block parallel methods for solving linear equations},
  journal = {IEEE Trans. on Computers},
  year = {1980},
  volume = {C-29},
  pages = {354--359},
  number = {5}
}

@ARTICLE{WOHL80,
  author = {R. Wohlgemuth and N. Waespe-$\check{S}$ar$\check{c}$evi$\grave{c}$},
  title = {Bilayers of phosphatidylglycerol. A deuterium and phosphorus {NMR}
	study of the head-group region.},
  journal = BCH,
  year = {1980},
  volume = { },
  pages = { }
}

@BOOK{AlIS79,
  title = {The Timeless Way of Building},
  publisher = {Oxford University Press},
  year = {1979},
  author = {C. Alexander and S. Ishikawa and M. Silverstein},
  address = {New York}
}

@ARTICLE{ARAU79,
  author = {P.S. de Araujo and M.Y. Rosseneu and J.M.H. Kremer and E.~J.~J.~van
	Zoelen and G.H. de Haas},
  title = {Structure and thermodynamic properties of the complexes between phospholipase
	{A$_2$} and lipid micelles},
  journal = BCH,
  year = {1979},
  volume = {18},
  pages = {580--586},
  annote = {monomer porcine PLA2 is fully active}
}

@ARTICLE{BLOO79,
  author = {M. Bloom},
  title = {Squishy proteins in fluid membranes},
  journal = {Can. J. Phys.},
  year = {1979},
  volume = {57},
  pages = {2227}
}

@ARTICLE{BROW79,
  author = {K. R. Brownstein and C. E. Tarr},
  title = {Importance of Classical Diffusion in {NMR} Studies of Water in Biological
	Cells},
  journal = {Physical Review A},
  year = {1979},
  volume = {19},
  pages = {2446--2453},
  number = {6},
  brief = {He gives a solution of the Bloch-diffusion eq. for transport across
	cell membranes. Very much related to our work.}
}

@ARTICLE{BULD79,
  author = {G. B{\"u}ldt and H. U. Gally and Joachim Seelig and G. Zacca\"{i}},
  title = {Neutron Diffraction Studies on Phosphatidylcholine Model Membranes.
	{I.} Head Group Conformation},
  journal = JMB,
  year = {1979},
  volume = {134},
  pages = {673--691},
  annote = {headgroup almost parallel to membrane surface in gel and LC phase},
  keywords = {experimental; membrane; DPPC; gel phase; LC phase; head group},
  suggestions = {look at orientation of headgroups; look at fluctuation in head group
	orientation (experimentally not accessible)}
}

@ARTICLE{DAVI79A,
  author = {M. A Davidovich and R. S. Knox},
  title = {On the Rate of Triplet Excitation Transfer in the Diffusive Limit},
  journal = CPL,
  year = {1979},
  volume = {68},
  pages = {391--394},
  number = {2,3}
}

@ARTICLE{DAVI79,
  author = {J.H. Davis},
  title = {Deuterium magnetic resonancestudy of the gel and liquid crystalline
	phases of dipalmitoyl phosphotidylcholine},
  journal = BJ,
  year = {1979},
  volume = {27},
  pages = {339--358}
}

@ARTICLE{GALL79,
  author = {H.-J. Galla and W. Hartmann and U. Theilen and Erich Sackmann},
  title = {On Two-Dimensional Passive Random Walk in Lipid Bilayers and Fluid
	Pathways in Biomembranes},
  journal = JMEB,
  year = {1979},
  volume = {48},
  pages = {215--236},
  annote = {Smoluchowski equation not valid in 2 dimensions for bimolecular reactions;
	chain length does not influence jump frequency, only temperature
	does; DPPC->POPC does make almost no difference; head group structure
	has no specific influence; D=0.036*10^-5 cm^2/s long range diffusion
	\@ 35^o C for DOPC computed from pyrene label diffusion; jump frq.
	\nu=2.9 * 10^8/s; estimates tilt angle for DOPC at 17deg.; lateral
	diffusion is thought to be facilitated by (kink) defect movement
	along the chains; good table with jump frequencies og labels},
  keywords = {membrane; diffusion; random walk; experimental+theorie; cholsterol;
	tilt; DOPC; Montroll theory; LC phase; free volume model; kinks}
}

@ARTICLE{GALL79A,
  author = {H. U. Gally and G. Pluschke and P. Overath and Joachim Seelig},
  title = {Structure of {\it Escherichia coli} membranes. Phospholipid conformation
	in model membranes and cells as studied by deuterium magnetic resonance},
  journal = BCH,
  year = {1979},
  volume = {18},
  pages = {5605--5610},
  annote = {requested Tx=19921022.}
}

@ARTICLE{HABE79,
  author = {R. Haberkorn and M.E. Michel-Beyerle},
  title = {On the mechanism of magnetic field effects in bacterial photosynthesis},
  journal = {Biophys.~J.},
  year = {1979},
  volume = {26},
  pages = {489--498}
}

@ARTICLE{HONI79A,
  author = {B. Honig and U. Dinur and K. Nakanishi and V. Balogh-Nair and M.
	Gawinowicz and M. Arnaboldi and M. Motto},
  title = {An External Point-Charge Model for Wavelength Regulation in Visual
	Pigments},
  journal = JACS,
  year = {1979},
  volume = {101},
  pages = {7084--7086}
}

@ARTICLE{HONI79,
  author = {B. Honig and T. Ebrey and R. Callender and U. Dinur and M. Ottolenghi},
  title = {Photoisomerization, Energy Storage, and Charge Separation: A Model
	for Light Energy Transduction in Visual Pigments and Bacteriorhodopsin},
  journal = PNAS,
  year = {1979},
  volume = {76},
  pages = {2503}
}

@ARTICLE{KANG79,
  author = {S.Y. Kang and H.S. Gutowsky and J.C. Hshung and R. Jacobs and T.E.
	King and D. Rice and E. Oldfield},
  title = {Nuclear magnetic resonance investigation of the cytochrome oxydase--phospholipid
	interaction. A new model for boundary lipid},
  journal = BCH,
  year = {1979},
  volume = {18},
  pages = {3257--3267}
}

@ARTICLE{KNAP79,
  author = {Ernst-Walter Knapp and Klaus Schulten},
  title = {Magnetic Field Effect on the Hyperfine-Induced Electron Spin Motion
	in Radicals Undergoing Diamagnetic--Paramagnetic Exchange},
  journal = JCP,
  year = {1979},
  volume = {71},
  pages = {1878--1883}
}

@ARTICLE{Krei79,
  author = {H.-O. Kreiss},
  title = {Problems with different time scales for odes},
  journal = SJNA,
  year = {1979},
  volume = {16},
  pages = {980--998}
}

@ARTICLE{KRIN79,
  author = {N. I. Krinsky},
  title = {Carotenoid Protection against Oxidation},
  journal = PAC,
  year = {1979},
  volume = {51},
  pages = {649--660}
}

@ARTICLE{LESK79,
  author = {Arthur M. Lesk},
  title = {Detection of {3D} Patterns of Atoms in Chemical Structures},
  journal = CACM,
  year = {1979},
  volume = {22},
  pages = {219--224}
}

@ARTICLE{NeFr79,
  author = {S. A. Newman and H. L. Frisch},
  title = {Dynamics of Skeletal Pattern Formation in Developing Chick Limb},
  journal = SCI,
  year = {1979},
  volume = {205},
  pages = {662--668},
  number = {4407}
}

@ARTICLE{ORLA79,
  author = {G. Orlandi and Klaus Schulten},
  title = {Coupling of Stereochemistry and Proton Donor--Acceptor Properties
	of a {Schiff} Base: A Model of a Light-Driven Proton Pump},
  journal = CPL,
  year = {1979},
  volume = {64},
  pages = {370--374}
}

@ARTICLE{OWIK79,
  author = {J. C. Owiki and R.M. McConnell},
  title = {Theory of protein--lipid and protein--protein interactions in bilayer
	membranes},
  journal = PNAS,
  year = {1979},
  volume = {76},
  pages = {5750}
}

@ARTICLE{OWIK78,
  author = {J.~C. Owiki and M.~W. Springgate and H.~M. McConnell},
  title = {Theoretical study of protein--lipid interactions in bilayer membranes},
  journal = PNAS,
  year = {1979},
  volume = {75},
  pages = {1616}
}

@ARTICLE{PEAR79,
  author = {R. H. Pearson and I. Pascher},
  title = {The molecular structure of lecithin dihydrate},
  journal = NAT,
  year = {1979},
  volume = {281},
  pages = {499--501},
  address = {London},
  annote = {X-ray structure of DMPC described; fist X-ray structure of a phosphatitylcholine;
	the two molecules in the unit cell are displaced by one zig-zag;
	area/head=38.9A^2; tilt=12^o; very low hydration (5%w/w water); T=10..15^o
	C; chain planes are alternating perpendicular/parallel; no chain
	tilt for DLPE; gives torsion angles for head and glycerol; head group
	tilt 17^o and 22^o; PN length 4.3A and 4.5A; head groups of the two
	molecules point in different directions; LC state is the usual one
	found in natural systems},
  keywords = {DMPC; LPPC; DLPE; experiment; membrane; X-ray; crystall phase; H-bonding
	network},
  suggestions = {look at length of PN vector; look at tilt of hydrocarbon chains; investigate
	differences of adjunct molecules: what is the symmetry; look at flexibility
	of C2-C3 glycerine bond}
}

@ARTICLE{PRIV79,
  author = {P.\ L.\ Privalov},
  title = {Stability of Proteins: Small Globular Proteins},
  journal = {Adv.\ Prot.\ Chem.},
  year = {1979},
  volume = {33},
  pages = {167--241}
}

@ARTICLE{RAHM79,
  author = {T.S. Rahman and R.S. Knox and V.M. Kenkre},
  title = {Theory of depolarization of fluorescence in molecular pairs},
  journal = {Chem.~Phys.},
  year = {1979},
  volume = {44},
  pages = {197--211}
}

@ARTICLE{RICE79,
  author = {D.M. Rice and M.D. Meadows and A.O. Scheinman and F.M. Goni and J.C.
	Gomez-Fernandez and M.A. Moscarello and D. Chapman and E. Oldfield},
  title = {A nuclear Magnetic resonance study of sarcoplasmic reticulum Ca$^{2+}$,
	Mg$^{2+}$-ATPase, lipophilin, and proteo-lipid apoprotein--lecithin
	systems and a comparison with the effects of cholesterol},
  journal = BCH,
  year = {1979},
  volume = {18},
  pages = {5893--5903}
}

@ARTICLE{SCHU79,
  author = {Klaus Schulten and Irving R. Epstein},
  title = {Recombination of Radical Pairs in High Magnetic Fields: A Path Integral--{M}onte
	{C}arlo Treatment},
  journal = JCP,
  year = {1979},
  volume = {71},
  pages = {309--316}
}

@ARTICLE{SMIT79,
  author = {I.C.P. Smith and K.W. Butler and A.P. Tulloch and J.H. Davis and
	M. Bloom},
  title = {The properties of gel state lipid membranes of {\it Acholeplasma
	laidlawii} as observed by deuterium nuclear magnetic resonance},
  journal = {FEBS Lett.},
  year = {1979},
  volume = {100},
  pages = {57--61}
}

@ARTICLE{SPER79,
  author = {W. Sperling and C. Rafferty and K. Kohl and N. Dencher},
  title = {Isomeric Composition of Bacteriorhodopsin under Different Environmental
	Light Conditions.},
  journal = FEBS,
  year = {1979},
  volume = {97},
  pages = {129--132}
}

@ARTICLE{SPER85,
  author = {W. Sperling and C. N. Rafferty and K. Kohl and N. A. Dencher},
  title = {Isomeric Composition of Bacteriorhodopsin under Different Environmental
	Light Conditions},
  journal = FEBS,
  year = {1979},
  volume = {97},
  pages = {129--132}
}

@ARTICLE{TAVA79,
  author = {Paul Tavan and Klaus Schulten},
  title = {The {$2^1A_g$ -- $1^1B_u$} Energy Gap in the Polyenes: An Extended
	Configuration Interaction Study},
  journal = JCP,
  year = {1979},
  volume = {70},
  pages = {5407--5413},
  number = {12},
  annote = {June 15}
}

@ARTICLE{TAVA79A,
  author = {Paul Tavan and Klaus Schulten},
  title = {Correlation Effects in the Spectra of Polyacenes},
  journal = JCP,
  year = {1979},
  volume = {70},
  pages = {5414--5421},
  number = {12},
  annote = {jun 15}
}

@ARTICLE{TERN79,
  author = {J. Terner and C. Hsieh and A. R. Burns and M. A. El-Sayed},
  title = {Time-resolved resonance Raman spectroscopy of intermediates of bacteriorhodopsin:
	The $bK_{590}$ intermediate},
  journal = PNAS,
  year = {1979},
  volume = {76},
  pages = {3046--3050}
}

@ARTICLE{THRA79,
  author = {R.J. Thrash and H.L.-B. Fang and G.E. Leroi},
  title = {On the role of forbidden low-lying excited states of light-harvesting
	carotenoids in photosynthesis},
  journal = PCPB,
  year = {1979},
  volume = {29},
  pages = {1049--1050}
}

@ARTICLE{VIEH79,
  author = {W. Viehmann},
  title = {The magnetic compass of blackcaps ({\em {S}ylvia atricapilla})},
  journal = {Behaviour},
  year = {1979},
  volume = {68},
  pages = {24--30}
}

@ARTICLE{WANG79,
  author = {K. Wang and J. McClure and A. Tu},
  title = {Major myofibrillar components of striated muscle},
  journal = PNAS,
  year = {1979},
  volume = {76},
  pages = {3698--3702}
}

@ARTICLE{WELL79,
  author = {J.A. Wells and R.G. Yount},
  title = {Active site trapping of nucleotides by crosslinking two sulfhydryls
	in myosin subfragment S1},
  journal = PNAS,
  year = {1979},
  volume = {76},
  pages = {4966--4970}
}

@ARTICLE{WLOD79,
  author = {A. Wlodawer and J. P. Segrest and B. H. Chung and Chiovetti, Jr.,
	R. and J. N. Weinstein},
  title = {High-Density Lipoprotein Recombinants: Evidence for a Bicycle Tire
	Micelle Structure Obtained by Neutron Scattering and Electron Microscopy},
  journal = FEBS,
  year = {1979},
  volume = {104},
  pages = {231--235}
}

@ARTICLE{ZACC79,
  author = {G. Zacca\"{\i} and G. B\"uldt and Anna Seelig and Joachim Seelig},
  title = {Neutron Diffraction Studies on Phosphatidylcholine Model Membranes.
	{I{}I.} Chain Conformation and Segmental Disorder},
  journal = JMB,
  year = {1979},
  volume = {134},
  pages = {693--706},
  annote = {expects all-trans state in gel phase; positional info on different
	C atoms},
  keywords = {experimental; membrane; DPPC; gel phase; LC phase; DPPC}
}

@BOOK{AbMa78,
  title = {Foundations of Mechanics},
  publisher = {Benjamin Cummins Publishing Co.},
  year = {1978},
  author = {R. Abraham and J.E. Marsden},
  address = {Reading, Massachusetts},
  edition = {2nd edition}
}

@ARTICLE{ANDE78,
  author = {Charles M. Anderson and Ronald E. Stenkamp and Robert C. McDonald
	and Thomas A. Steitz},
  title = {A Refined Model of the Sugar Binding Site of Yeast Hexokinase {B}},
  journal = JMB,
  year = {1978},
  volume = {123},
  pages = {207--219}
}

@ARTICLE{ANDE78A,
  author = {C. M. Anderson and R. E. Stenkamp and T. A. Steitz},
  title = {Sequencing a Protein by {X}-ray Crystallography},
  journal = JMB,
  year = {1978},
  volume = {123},
  pages = {1--13}
}

@ARTICLE{ANDR78,
  author = {J.R. Andrews and B.S. Hudson},
  title = {Environmental effects on radiative rate constants with applications
	to linear polyenes},
  journal = JCP,
  year = {1978},
  volume = {68},
  pages = {4587--4594}
}

@BOOK{Arno78,
  title = {Mathematical Methods of Classical Mechanics},
  publisher = {Springer-Verlag},
  year = {1978},
  author = {V. I. {Arnol'd}},
  nremark = {CALL NO: 531.01AR6M:EV1989}
}

@ARTICLE{BECH78,
  author = {B.~Becher and F.~Tokunaga and T.~G.~Ebrey},
  title = {Ultraviolet and visible absorption spectra of the purple membrane
	protein and the photocycle intermediates},
  journal = BCH,
  year = {1978},
  volume = {17},
  pages = {2293--2300}
}

@ARTICLE{BELL78,
  author = {G. I. Bell},
  title = {Models for the Specific Adhesion of Cells to Cells},
  journal = SCI,
  year = {1978},
  volume = {200},
  pages = {618--627}
}

@ARTICLE{BENN78,
  author = {W. S. Bennett and T. A. Steitz},
  title = {Glucose-induced conformational change in yeast hexokinase},
  journal = BCH,
  year = {1978},
  volume = {75},
  pages = {4848--4852}
}

@ARTICLE{BREW78,
  author = {H.B. Brewer and T. Fairwell and A. Larue and R. Ronan and A. Houser
	and T.J. Bronzer},
  title = {The Amino Acid Sequence of Human apo{A-I}, An Apolipoprotein isolated
	from high density lipoproteins},
  journal = {Biochem. Biophys. Res. Commun.},
  year = {1978},
  volume = {80},
  pages = {623}
}

@ARTICLE{BULD78,
  author = {G. B{\"u}ldt and H. U. Gally and Anna Seelig and Joachim Seelig and
	G. Zacca{\"{\i}}},
  title = {Neutron diffraction studies on selectively deuterated phospholipid
	bilayers},
  journal = NAT,
  year = {1978},
  volume = {271},
  pages = {182--184},
  annote = {headgroup almost parallel to bilayer in gel and LC phase; gives data
	on positions of different Cs in different phases, with variing temperature
	and water content; the two carbon chains are out of step by 1.8A
	= 1.5C-C distance},
  keywords = {experimental; membrane; DPPC; gel; LC phase},
  suggestions = {study the distance of the headgroup atoms to the center}
}

@ARTICLE{Chan78,
  author = {D.~Chandler},
  title = {Statistical Mechanics of Isomerization dynamics in Liquids and Transition-State
	Approximation},
  journal = JCP,
  year = {1978},
  volume = {68},
  pages = {2959--70},
  number = {6}
}

@ARTICLE{CHOU78,
  author = {Chou and P. Y. and Fasman and G. D.},
  title = {Prediction of the secondary structure of proteins from their amino
	acid sequence.},
  journal = {Adv. in Enzymology},
  year = {1978},
  volume = {47},
  pages = {45--148}
}

@BOOK{DUBR78,
  title = {The Geomagnetic Field and Life},
  publisher = {Plenum Press},
  year = {1978},
  editor = {Brown, Jr., F. A.},
  author = {A. P. Dubrov},
  address = {New York}
}

@ARTICLE{EICK78,
  author = {T.~H.~Eickbrusch and E.~N.~Moudrianakis},
  title = {The histone core complex: an octamer assembled by two sets of protein--protein
	interactions},
  journal = BCH,
  year = {1978},
  volume = {17},
  pages = {4955},
  annote = {instability of the dimer to tetramer}
}

@ARTICLE{ErMc78,
  author = {Donald L. Ermak and J. A. McCammon},
  title = {Brownian Dynamics with Hydrodynamic Interactions},
  journal = {J. Chem.\ Phys.},
  year = {1978},
  volume = {69},
  pages = {1352--1360},
  number = {4}
}

@ARTICLE{Fixm78,
  author = {M. Fixman},
  title = {Simulation of Polymer Dynamics. {I}. {G}eneral Theory},
  journal = {J. Chem.\ Phys.},
  year = {1978},
  volume = {69},
  pages = {1527--1537},
  where = {TB lib}
}

@ARTICLE{GARN78,
  author = {J. Garnier and D.J. Osguthorpe and B. Robson},
  title = {Analysis of the accuracy and implications of simple methods for predicting
	the secondary structure of globular proteins},
  journal = JMB,
  year = {1978},
  volume = {120},
  pages = {97}
}

@BOOK{GRAN78,
  title = {Dielectric Behaviour of Biological Macromolecules in Solution},
  publisher = {Clarendon Press},
  year = {1978},
  author = {E. H. Grant and R. J. Sheppard and G. P. South},
  address = {Oxford}
}

@ARTICLE{HEND78,
  author = {R.~Henderson and J.~S.~Jubb and S.~Whytock},
  title = {Specific labeling of the protein and lipid on the extracellular surface
	of purple membrane.},
  journal = JMB,
  year = {1978},
  volume = {123},
  pages = {259--274}
}

@ARTICLE{HOAR78,
  author = {C. A. R. Hoare},
  title = {Communicating Sequential Processes},
  journal = CACM,
  year = {1978},
  volume = {21},
  pages = {666--677},
  number = {8},
  keywords = {occam}
}

@ARTICLE{JOST73,
  author = {P.C. Jost and O.H. Griffith and R.A. Capaldi and G. Vanderkooi},
  title = {Evidnece for boundary lipids in membranes},
  journal = PNAS,
  year = {1978},
  volume = {70},
  pages = {480--484}
}

@ARTICLE{KABS78,
  author = {W. Kabsch},
  title = {A discussion of the solution for the best rotation to relate two
	sets of vectors},
  journal = ACA,
  year = {1978},
  volume = {34},
  pages = {827--828}
}

@ARTICLE{LEVI78,
  author = {M. Levitt},
  title = {Conformational Preference of Amino Acids in Globular Proteins},
  journal = {Biochemistry},
  year = {1978},
  volume = {17},
  pages = {4277}
}

@INCOLLECTION{LOZI78,
  author = {R. H. Lozier and W. Niederberger and M. Ottolenghi and G. Sivorinovsky
	and J. W. Stoechenius},
  title = {On the Photocycle of Light- and Dark-Adapted Bacteriorhodopsin},
  booktitle = {Energetics and Structure of Halophilic Microorganisms},
  publisher = {North Holland Biomedical Press},
  year = {1978},
  editor = {S. R. J. Caplan and M. Ginzburg},
  pages = {123--141},
  address = {Elsevier}
}

@ARTICLE{MANN78,
  author = {G. S. Manning},
  title = {The molecular theory of polyelectrolyte solutions with applications
	to the electrostatic properties of polynucleotides},
  journal = QRB,
  year = {1978},
  volume = {2},
  pages = {179--246},
  annote = {manning polyelectric theory}
}

@ARTICLE{MASO78,
  author = {R.P. Mason and C.F. Polnaszek},
  title = {Spin-label and deuterium order parameter discrepancies in bilayers:
	one possible explanation},
  journal = BCH,
  year = {1978},
  volume = {17},
  pages = {1758}
}

@ARTICLE{MCIN78,
  author = {T.~J. Mcintosh},
  title = {The effect of cholesterol on the structure of phosphatidylcholine
	bilayers},
  journal = BBA,
  year = {1978},
  volume = {513},
  pages = {43--58},
  annote = {Stiudies of choletral membrane Classic experimental. Maybe good for
	Sheng?}
}

@ARTICLE{OHMI78,
  author = {I. Ohmine and Martin Karplus and Klaus Schulten},
  title = {Renormalized Configuration Interaction Method for Electron Correlation
	in the Excited States of Polyenes},
  journal = JCP,
  year = {1978},
  volume = {68},
  pages = {2298--2318},
  number = {5},
  annote = {March 1}
}

@ARTICLE{OLDF78,
  author = {E. Oldfield and R. Gilmore and M. Glaser and H.S. Gutowsky and J.C.
	Hshung and S.Y. Kang and T.E. King and M. Meadows and D. Rice},
  title = {Deuterium nuclear magnetic resonance investigation of the effects
	of proteins and polypeptides on hydrocarbon chain order in model
	membrane systems},
  journal = PNAS,
  year = {1978},
  volume = {15},
  pages = {4145--4151}
}

@ARTICLE{REMI78,
  author = {Stephen J. Remington and Brian W. Mathews},
  title = {A general method to assess similarity of protein structures, with
	applications to {T4} bacteriophage lysozyme},
  journal = PNAS,
  year = {1978},
  volume = {75},
  pages = {2180--2184}
}

@ARTICLE{RyBe78,
  author = {J.-P. Ryckaert and A. Bellemans},
  title = {Molecular dynamics of liquid alkanes},
  journal = {Faraday Discussions},
  year = {1978},
  volume = {66},
  pages = {95--106}
}

@ARTICLE{SCHR78,
  author = {Thomas Schreckenbach and B{\"a}rbel Walckhoff and Dieter Oesterhelt},
  title = {Specificity of the Retinal Binding Site of Bacteriorhodopsin: {C}hemical
	and Stereochemical Requirements for the Binding of Retinol and Retinal},
  journal = BCH,
  year = {1978},
  volume = {17},
  pages = {5353--5359}
}

@INCOLLECTION{SCHU78B,
  author = {Klaus Schulten},
  title = {An Isomerization Model for the Photocycle of Bacteriorhodopsin},
  booktitle = {Energetics and Structure of Halophilic Organisms},
  publisher = {Elsevier},
  year = {1978},
  editor = {S. R. Caplan and M. Ginzburg},
  pages = {331--334}
}

@ARTICLE{SCHU78C,
  author = {Klaus Schulten and Charles E. Swenberg and Albert Weller},
  title = {A Biomagnetic Sensory Mechanism Based on Magnetic Field Mo\-dulated
	Coherent Electron Spin Motion},
  journal = ZPC,
  year = {1978},
  volume = {NF111},
  pages = {1--5}
}

@ARTICLE{SCHU78,
  author = {Klaus Schulten and Paul Tavan},
  title = {A Mechanism for the Light-Driven Proton Pump of\begin{em} {H}alobacterium
	halobium\end{em}},
  journal = NAT,
  year = {1978},
  volume = {272},
  pages = {85--86}
}

@ARTICLE{SCHU78A,
  author = {Klaus Schulten and Albert Weller},
  title = {Exploring Fast Electron Transfer Processes by Magnetic Fields},
  journal = BJ,
  year = {1978},
  volume = {24},
  pages = {295--305}
}

@ARTICLE{SCHU78D,
  author = {Klaus Schulten and Peter G. Wolynes},
  title = {Semiclassical Description of Electron Spin Motion in Radicals Including
	the Effect of Electron Hopping},
  journal = JCP,
  year = {1978},
  volume = {68},
  pages = {3292--3297}
}

@ARTICLE{SCOT78,
  author = {H.L. Scott and S.-L. Cherng},
  title = {{M}onte {C}arlo studies of phospholipid lamellae. Effects of proteins,
	cholesterol, bilayer curvature and lateral mobility on order parameters},
  journal = BBA,
  year = {1978},
  volume = {510},
  pages = {209--215}
}

@ARTICLE{SEEL78b,
  author = {A. Seelig and J. Seelig},
  title = {Lipid--protein interaction in reconstituted cytochrome C oxidase
	phospholipid membranes},
  journal = {Hoppy-Seyler's Z. Physiol. Chem.},
  year = {1978},
  volume = {359},
  pages = {1747--1756}
}

@ARTICLE{SEEL78,
  author = {J. Seelig},
  title = {Phosphorus-31 neuclear magnetic resonance and the head-group structure
	of phospholipids in membranes},
  journal = BBA,
  year = {1978},
  volume = {505},
  pages = {105--141}
}

@ARTICLE{SEEL78A,
  author = {Joachim Seelig and Nada Waespe-{\v S}ar\v{c}evi\`{c}},
  title = {Molecular Order in Cis and Trans Unsaturated Phospholipid Bilayers},
  journal = BCH,
  year = {1978},
  volume = {17},
  pages = {3310--3315},
  number = {16},
  annote = {C=C bond vector almost parallel to bilayer normal at $9^o$; biological
	membranes have a high percentage of unsaturated cis lipids; T=27^oC;
	difference at C2 position of sn-2 /sn-1 chain is a general feature:
	sn-1 chain is perpendicular to surface in all segments, while sn-2
	chain is first parallel and then bends over; the main finding of
	this paper is that after correction for the different orientation
	of the C=C bond, the fluctuation part of the order parameter is thought
	to be the same as in the saturated chain and should only depend on
	the distance from the chain anchor. However, the errormargins here
	are quite high. this finding is in disagreement with our finding.},
  keywords = {experimental; POPC; cis/trans},
  suggestions = {Seelig sees possible indication for two different conformations of
	POPC, but can not decide with his data: look and see if we can isloate
	two different conformations (analog to DLPE \cite{PEAR79}); determine
	the orientation of the C=C vector (here \pm 9^o) and compare; report
	this explanation in paper, relate RMS values to order parameters;
	look for bend in C2 position of the sn-2 chain}
}

@BOOK{BULI78,
  title = {{N}umerische {M}athematik},
  publisher = {Springer},
  year = {1978},
  author = {Stoer and Bulirsch},
  volume = {II},
  series = {Heidelberger Taschenb\"ucher},
  address = {Berlin, Heidelberg, New York},
  edition = {2}
}

@ARTICLE{StTS78,
  author = {W. B. Streett and D.J. Tildesley and G. Saville},
  title = {Multiple time step methods in molecular dynamics},
  journal = {Mol. Phys.},
  year = {1978},
  volume = {35},
  pages = {639--648}
}

@ARTICLE{STRE78,
  author = {W. B. Streett and D.~J. Tildesley and G. Saville},
  title = {Multiple time-step methods in molecular dynamics},
  journal = MP,
  year = {1978},
  volume = {35},
  pages = {639--648},
  number = {3},
  annote = {speedup of 3...8; modest increase in storage requirement; uses Tailor
	series to approximate the force from the outer distance classes;
	thorough, good analysis; only Lennard Jones potential},
  keywords = {fluid simulation; distance class algorithm; LJ-potential}
}

@ARTICLE{TAVA78,
  author = {Paul Tavan and Klaus Schulten},
  title = {The `Phantom' Photochemical Singlet State of Stilbene and its Diphenylpolyene
	Relative},
  journal = CPL,
  year = {1978},
  volume = {56},
  pages = {200--204},
  number = {2},
  annote = {june 1}
}

@ARTICLE{WARS78,
  author = {A. Warshel},
  title = {Charge Stabilization Mechanism in the Visual and Purple Membrane
	Pigments},
  journal = PNAS,
  year = {1978},
  volume = {75},
  pages = {2558--2562}
}

@ARTICLE{WERN78,
  author = {Hans-Joachim Werner and Klaus Schulten and Albert Weller},
  title = {Electron Transfer and Spin Exchange Contributing to the Magnetic
	Field Dependence of the Primary Photochemical Reaction of Bacterial
	Photosynthesis},
  journal = BBA,
  year = {1978},
  volume = {502},
  pages = {255--268}
}

@ARTICLE{WILS78,
  author = {J.C. Wilschut and J. Regts and H. Westenberg and G. Scherphof},
  title = {Action of phospholipase {A$_2$} on phosphatidylcholine bilayers.
	{Effects} of the phase transition, bilayer curvature and structural
	defects.},
  journal = BBA,
  year = {1978},
  volume = {508},
  pages = {185--196}
}

@INPROCEEDINGS{WILT78,
  author = {W. Wiltschko},
  title = {Further Analysis of the Magnetic Compass of Migratory Birds},
  booktitle = {Animal Migration, Navigation, and Homing},
  year = {1978},
  editor = {K. Schmidt-Koenig and W.T. Keeton},
  pages = {302--310},
  address = {Berlin},
  publisher = {Springer}
}

@ARTICLE{ATON77,
  author = {B.~Aton and A.~G.~Doukas and R.~H.~Callender and B.~Becker and T.~G.~Ebrey},
  title = {Resonance Raman Studies of the Purple Membrane},
  journal = BCH,
  year = {1977},
  volume = {16},
  pages = {2995--2999}
}

@ARTICLE{BERN77,
  author = {F.~C. Bernstein and T.~F. Koetzle and G.~J. Williams and E.~F. Meyer
	and M.~D. Brice and J.~R. Rogers and O. Kennard and T. Shimanouchi
	and M. Tasumi},
  title = {The {P}rotein {D}ata {B}ank: A Computer-Based Archival File for Macromolecular
	Structures},
  journal = JMB,
  year = {1977},
  volume = {112},
  pages = {535--542}
}

@ARTICLE{BEZA77,
  author = {F.~Bezanilla and C.~M.~Armstrong},
  title = {Inactivation of the sodium channel. {I}. Sodium current experiments},
  journal = JGP,
  year = {1977},
  volume = {70},
  pages = {549--566},
  annote = {first introduces the idea of the interaction between the ion and
	the carbonyl oxygen atoms}
}

@ARTICLE{Book77,
  author = {M.A. Bookman},
  title = {Sensitivity of the homing pigeon to an earth-strength magnetic field},
  journal = NAT,
  year = {1977},
  volume = {267},
  pages = {340--342}
}

@ARTICLE{BURK77,
  author = {M. Burke and E. Reisler},
  title = {Effect of nucleotide binding on the proximity of the essential sulfhydryl
	groups of myosin: Chemical probing of movement of residues during
	conformational transitions},
  journal = BCH,
  year = {1977},
  volume = {16},
  pages = {5559--5563}
}

@ARTICLE{CREI77,
  author = {T. E. Creighton},
  title = {Energetics of Folding and Unfolding of Pancreatic Trypsin Inhibitor},
  journal = JMB,
  year = {1977},
  volume = {113},
  pages = {295--312}
}

@ARTICLE{DOVE77,
  author = {S.~D.~Dover},
  title = {Symmetry and packing in {B-DNA}},
  journal = JMB,
  year = {1977},
  volume = {110},
  pages = {699--700},
  annote = {ref'd as 841 in saenger's book, page 240 says 10bp/turn in xstal}
}

@ARTICLE{EBRE77,
  author = {T. G. Ebrey and B. Becher and B. Mao and P. Kilbride and B. Honig},
  title = {Exciton Interactions and Chromophore Orientation in the Purple Membrane},
  journal = JMB,
  year = {1977},
  volume = {112},
  pages = {377--397}
}

@ARTICLE{EDMA77,
  author = {K. A. P. Edman and J. C. Hwang},
  title = {The force-velocity relationship in vertebrate muscles at varied tonicity
	of the extracellular medium},
  journal = {J. Physiol. (Lond.)},
  year = {1977},
  volume = {15},
  pages = {335}
}

@ARTICLE{ELDE77,
  author = {M. Elder and P. Hitchcock and R. Mason and G. G. Shipley},
  title = {A refinement analysis of the crystallography of the phospholipid,
	1,2-dilauroyl-DL-phosphatidylethanolamine, and some remarks on lipid--lipid
	and lipid--protein interactions},
  journal = PRSLA,
  year = {1977},
  volume = {354},
  pages = {157--170},
  annote = {requested Tx=19920908.}
}

@ARTICLE{Evan77,
  author = {D.~J.~Evans},
  title = {On the Representation of Orientation Space},
  journal = {Mol.\ Phys.},
  year = {1977},
  volume = {34},
  pages = {317--325},
  number = {2}
}

@ARTICLE{FINC77,
  author = {J.~T.~Finch and L.~C.~Lutter and D.~Rhodes and R.-J.~Brown and B.~Ruston
	and M.~Levitt and A.~Klug},
  title = {Structure of nucleosome core particles of chromatin},
  journal = NAT,
  year = {1977},
  volume = {269},
  pages = {29--36}
}

@ARTICLE{FORD77,
  author = {L. E. Ford and A. F. Huxley and R. M. Simmons},
  title = {Tension responses to sudden length change in stimulated frog muscle
	fibers near slack length},
  journal = {J. Physiol. (Lond.)},
  year = {1977},
  volume = {269},
  pages = {441}
}

@BOOK{FoMM77,
  title = {Computer Methods for Mathematical Computations},
  publisher = {Prentice-Hall},
  year = {1977},
  author = {G. H. Forsythe and M. A. Malcolm and C. B. Moler},
  address = {Englewood Cliffs, N.~J.}
}

@ARTICLE{GUNS77,
  author = {W. F. van Gunsteren and H. J. C. Berendsen},
  title = {Algorithms for Macromolecular Dynamics and Constraint Dynamics},
  journal = MP,
  year = {1977},
  volume = {34},
  pages = {1311--1327},
  number = {5},
  annote = {Eine echte Goldgrube! Says angle constraints are no good. Verlet
	is best integrator. Uses SHAKE.}
}

@ARTICLE{VaBe77,
  author = {W.~F. van Gunsteren and H.~J.~C. Berendsen},
  title = {Algorithms for Macromolecular Dynamics and Constraint Dynamics},
  journal = {Molecular Phys},
  year = {1977},
  volume = {34},
  pages = {1311--1327}
}

@ARTICLE{HABE77,
  author = {R. Haberkorn},
  title = {Theory of magnetic field modulation of radical recombination reactions
	{I}},
  journal = {Chem.~Phys.},
  year = {1977},
  volume = {19},
  pages = {165--179}
}

@ARTICLE{HEND77,
  author = {Henderson, R.},
  title = {The Purple Membrane from {{\em Halobacterium halobium}}},
  journal = ARBB,
  year = {1977},
  volume = {6},
  pages = {87--109}
}

@ARTICLE{HOFF77,
  author = {A. J. Hoff and H. Rademaker and R. van Grondelle and L. N. M. Duysens},
  title = {On the Magnetic Field Dependence of the Yield of the Triplet State
	in Reaction Centers of Photosynthetic Bacteria},
  journal = BBA,
  year = {1977},
  volume = {460},
  pages = {547--554}
}

@ARTICLE{HONG77,
  author = {F.T. Hong},
  title = {Phototelectric and magneto-orientation effects in pigmented biological
	membranes},
  journal = {J.~Colloid Surf.~Sci.},
  year = {1977},
  volume = {58},
  pages = {471--497}
}

@ARTICLE{HUBE77,
  author = {D.~Hubel and T.~N. Wiesel and S.~LeVay},
  title = {Plasticity of ocular dominance columns in monkey striate cortex},
  journal = {Phil. Trans. Roy. Soc. Lond. B},
  year = {1977},
  volume = {278},
  pages = {377--409}
}

@ARTICLE{KALI77,
  author = {O. Kalisky and C. R. Goldschmidt and M. Ottolenghi},
  title = {On the Photocycle and Light Adaptation of Dark-adapted Bacteriorhodopsin},
  journal = BJ,
  year = {1977},
  volume = {19},
  pages = {185--189}
}

@INCOLLECTION{KNOX77,
  author = {R. S. Knox},
  title = {Photosynthetic Efficiency and Exciton Transfer and Trapping},
  booktitle = {Primary Processes of Photosynthesis},
  publisher = {Elsevier},
  year = {1977},
  editor = {J. Barber},
  pages = {55--97},
  address = {Amsterdam}
}

@ARTICLE{KORE77,
  author = {R. Korenstein and B. Hess},
  title = {Hydration Effects on {\it cis-trans} Isomerization of Bacteriorhodopsin},
  journal = FEBS,
  year = {1977},
  volume = {82},
  pages = {7--11}
}

@ARTICLE{KRIE77,
  author = {A. Kriebel and A. Albrecht},
  title = {Excitonic Interaction Among Three Chromophores: An Application to
	the Purple Membrane of {{\em Halobacterium halobium}}},
  journal = JCP,
  year = {1977},
  volume = {65},
  pages = {4575--4583}
}

@ARTICLE{LEAS77,
  author = {M.J.M. Leask},
  title = {A physicochemical mechanism for magnetic field detection by migratory
	birds and homing pigeons},
  journal = NAT,
  year = {1977},
  volume = {267},
  pages = {144--145}
}

@ARTICLE{MANT77,
  author = {H.H. Mantsch and H. Saito and I.C.P. Smith},
  title = {Deuterium magnetic resonance. Applications in {\it chemistry, physics
	and biology}},
  journal = {Progr. {NMR} Spectroscopy},
  year = {1977},
  volume = {11},
  pages = {211--272}
}

@ARTICLE{MARU77,
  author = {K. Maruyama and S. Matsubara and R. Natori and Y. Nonomura and S
	Kimura and K. Ohashi and F. Murakami and K. Handa and G. Eguchi},
  title = {Connectin, a elastic protein of muscle: Characterization and function},
  journal = JB,
  year = {1977},
  volume = {82},
  pages = {317--337}
}

@ARTICLE{MCCA77,
  author = {J. Andrew McCammon and Bruce R. Gelin and Martin Karplus},
  title = {Dynamics of Folded Proteins},
  journal = NAT,
  year = {1977},
  volume = {267},
  pages = {585--590},
  annote = {very early MD simulation},
  keywords = {BPTI}
}

@INPROCEEDINGS{MCLA77,
  author = {S. Mc{L}aughlin},
  title = {Electrostatic potentials at membrane-solution interfaces},
  booktitle = {Current topics in membranes and transport},
  year = {1977},
  editor = {F. Bronner and A. Kleinzeller},
  volume = {9},
  pages = {71--144},
  address = {New York},
  publisher = {Academic press}
}

@ARTICLE{MONG77,
  author = {T.G. Monger and W.W. Parson},
  title = {Singlet-triplet fusion in {{\em {R}hodopseudomonas sphaeroides}}
	chromatophores. A probe of the organization of the photosynthetic
	apparatus},
  journal = BBA,
  year = {1977},
  volume = {460},
  pages = {393--407}
}

@ARTICLE{MORA77,
  author = {V. V. Morariu and G. Benga},
  title = {Evaluation of a Nuclear Magnetic Resonance Technique for the Study
	of Water Exchange Through Erythrocyte Membranes in Normal and Pathological
	Subjects},
  journal = {Biochim.~Biophys.~Acta},
  year = {1977},
  volume = {{\bf 469}},
  pages = {301--310}
}

@ARTICLE{OHNO77,
  author = {K. Ohno and Y. Takeuchi and M. Yoshida},
  title = {Effect of Light-Adaptation on the Photoreaction of Bacteriorhodopsin
	from {{\em Halobacterium halobium}}.},
  journal = BBA,
  year = {1977},
  volume = {462},
  pages = {575--582}
}

@ARTICLE{PETE77,
  author = {N.O. Peterson and S.I. Chan},
  title = {More on the motional state of lipid bilayer membranes: interpretation
	of order parameters obtained from {N}uclear {M}agnetic {R}esonance
	experiments},
  journal = BCH,
  year = {1977},
  volume = {16},
  pages = {2657--2667}
}

@ARTICLE{PETT77,
  author = {M.J.~Pettei and A.P.~Yudd and K.~Nakanishi and R.~Henselman and W.~Stoeckenius},
  title = {Identification of Retinal Isomers Isolated from Bacteriorhodopsin},
  journal = BCH,
  year = {1977},
  volume = {16},
  pages = {1955--1959}
}

@ARTICLE{PHIL77,
  author = {J. B. Phillips},
  title = {Use of the Earth's Magnetic Field by Orienting Cave Salamanders (Eurycea
	lucifiga)},
  journal = {J. Comp. Physiol. A},
  year = {1977},
  volume = {121},
  pages = {273--288}
}

@ARTICLE{PILK77,
  author = {Frank G. Pilkiewicz and Michael J. Pettel and Anthony P. Yudd and
	Koji Nakanishi},
  title = {A Simple and Non-isomerizing Procedure for the Identification of
	Protein-linked Retinals},
  journal = {Exp.\ Eye Res.},
  year = {1977},
  volume = {24},
  pages = {421--423}
}

@ARTICLE{POPL77,
  author = {J. Pople and R. Seeger and R. Krishnan},
  title = {Variational Configuration Interaction Methods and Comparison with
	Pertubation Theory.},
  journal = IJQCS,
  year = {1977},
  volume = {11},
  pages = {149}
}

@ARTICLE{POWE77,
  author = {M. J. D. Powell},
  title = {Restart Procedures for the Conjugate Gradient Method},
  journal = {Mathematical Programming},
  year = {1977},
  volume = {12},
  pages = {241--254},
  annote = {powell minimization algorithm from X-PLOR}
}

@ARTICLE{POWN77,
  author = {H.J. Pownall and F.J. Hsu and M. Rosseneu and H. Peeters and A.M.
	Gotto and R.L. Jackson},
  title = {Thermodynamics of Helix formation in the Association of High Density
	Lipoprotein {A-I (Apo A-I)} to Dimyristoyl Phosphatidylcholin},
  journal = {Biochem. Biophys. Acta},
  year = {1977},
  volume = {488},
  pages = {190}
}

@ARTICLE{ROBE77,
  author = {M. F. Roberts and R. A. Deems and E. A. Dennis},
  title = {Dual role of interfacial phospholipid in phospholipase {A}$_2$ catalysis},
  journal = PNAS,
  year = {1977},
  volume = {74},
  pages = {1950--1954},
  annote = {get it}
}

@ARTICLE{RyCB77,
  author = {J.P. Ryckaert and G. Ciccotti and H.J.C. Berendsen},
  title = {Numerical integration of the {C}artesian equation of motion of a
	system with constraints: molecular dynamics of n-alkanes},
  journal = JCP,
  year = {1977},
  volume = {23},
  pages = {327--341},
  annote = {Description of the {SHAKE} Algorithm}
}

@ARTICLE{SCHR77,
  author = {Thomas Schreckenbach and B{\"a}rbel Walckhoff and Dieter Osterhelt},
  title = {Studies on the Retinal-Protein Interaction in Bacteriorhodopsin},
  journal = EJB,
  year = {1977},
  volume = {76},
  pages = {499--511},
  annote = {gives bR reconstitution rates}
}

@ARTICLE{SCHU77,
  author = {Klaus Schulten},
  title = {Quantum Mechanical Propensity Rules for the Transfer of Angular Momentum
	in Three-Atom Reactions},
  journal = BBG,
  year = {1977},
  volume = {81},
  pages = {166--168}
}

@ARTICLE{SCHU77A,
  author = {Zan Schulten and Klaus Schulten},
  title = {The Generation, Diffusion, Spin Motion, and Recombination of Radical
	Pairs in Solution in the Nanosecond Time Domain},
  journal = JCP,
  year = {1977},
  volume = {66},
  pages = {4616--4634}
}

@ARTICLE{SCOT77,
  author = {H.L. Scott},
  title = {{M}onte {C}arlo studies of the hydrocarbon region of lipid bilayers},
  journal = BBA,
  year = {1977},
  volume = {469},
  pages = {264}
}

@ARTICLE{SEEL77A,
  author = {Anna Seelig and Joachim Seelig},
  title = {Effect of a Single Cis Double Bond on the Structure of a Phospholipid
	Bilayer},
  journal = BCH,
  year = {1977},
  volume = {16},
  pages = {45--50},
  number = {1},
  annote = {palmitoyl order parameter shape similar to DPPC; order params are
	generally lower than in DPPC; good intro on why to study POPC; LC
	phase is the biologically relevant one; POPC one of the most common
	naturally occuring lipids (70% in egg yolk lecithin); transition
	temp -5^o C; length of POPC more reduced compared to DPPC; the two
	chains are not equivalent; double bond has large effect in 9,10 position
	(where it naturally is); d-NMR averages frequencies down to 10^-5Hz,
	so it might be that our order params are higher because we do not
	include these low frequency motions},
  keywords = {POPC; experimental; membrane; order parameters},
  suggestions = {incorporate these exp. data in our plots}
}

@ARTICLE{SEEL77,
  author = {Joachim Seelig},
  title = {Deuterium magnetic resonance: Theory and application to lipid membranes},
  journal = QRB,
  year = {1977},
  volume = {10},
  pages = {353--418},
  annote = {requested Tx=19921015., re-requested Tx=19921028.; contains order
	parameter profiles for POPC},
  keywords = {POPC; order parameter; membrane}
}

@ARTICLE{SIMO77,
  author = {S. A. Simon and W. L. Stone and P. Busto-Latorre},
  title = {A Thermodynamic study of the partition of {\it n}-hexane into phosphotidylcholine-cholestral
	bilayers},
  journal = BBA,
  year = {1977},
  volume = {468},
  pages = {378--388},
  annote = {Partion coefficient of {\it n}-hexane from water into hexane or into
	bilayers are measured. Incoporation of cholestral into bilayers decreased
	the partition coefficient by a factor of 2.5. The thermodynamic transfer
	parameters were compared, showing liquid hydrocarbon is not a good
	model for bilayers whereas sodium dedecyl sulphate is a better model.
	Incooporation into bilayer is favored enthalpically but unfavored
	entropically, probably due to a restriction in the more ordered lipid
	membrane. The entropy change from hexane to bilayer is 60% of the
	entropy change of liquid to solid phase transition for hexane. The
	author suggest hexane on average aligns along the acyl chains.}
}

@ARTICLE{SPER77,
  author = {W. Sperling and P. Carl and C. N. Rafferty and N. A. Dencher},
  title = {Photochemistry and Dark Equilibrium of Retinal Isomers and Bacteriorhodopsin
	Isomers},
  journal = BSM,
  year = {1977},
  volume = {3},
  pages = {79--94}
}

@ARTICLE{STIG77,
  author = {D. Stigter},
  title = {Interactions of highly charged colloidal cylinders with application
	to double-stranded {DNA}},
  journal = BP,
  year = {1977},
  volume = {16},
  pages = {1435--1448}
}

@ARTICLE{TEN77,
  author = {Ten Eyck, L. F.},
  title = {Efficient structure-factor calculation for large molecules by the
	fast {Fourier} transform},
  journal = {Acta Cryst.},
  year = {1977},
  volume = {A33},
  pages = {486--492}
}

@ARTICLE{TORR77,
  author = {Torrie and Valleau},
  title = {Nonphysical sampling distributions in {M}onte {C}arlo free-energy
	estimation: Umbrella Sampling},
  journal = JCMP,
  year = {1977},
  volume = {23},
  pages = {187--199}
}

@ARTICLE{WERN77,
  author = {Hans-Joachim Werner and Zan Schulten and Klaus Schulten},
  title = {Theory of the Magnetic Field Modulated Geminate Recombination of
	Radical Ion Pairs in Polar Solvents: Application to the Pyrene-{N,N}-Dimethylaniline
	System},
  journal = JCP,
  year = {1977},
  volume = {67},
  pages = {646--663}
}

@BOOK{ASHC76,
  title = {Solid State Physics},
  publisher = {W. B. Saunders},
  year = {1976},
  author = {Neil W. Ashcroft and N. David Mermin},
  address = {Philadelphia}
}

@ARTICLE{BARK76,
  author = {J. A. Barker and D. Henderson},
  title = {{W}hat is ``liquid''? {U}nderstanding the states of matter},
  journal = RMP,
  year = {1976},
  volume = {48},
  pages = {587--676},
  number = {4},
  annote = {I don't have the article, as it is over 50 pages long and not very
	interesting: a general overview.}
}

@ARTICLE{Beem76,
  author = {D. Beeman},
  title = {Some Multistep Methods for use in Molecular Dynamics Calculations},
  journal = {J. Comput. Phys.},
  year = {1976},
  volume = {20},
  pages = {130--139}
}

@BOOK{BLUN76,
  title = {Protein Crystallography},
  publisher = {Academic Press},
  year = {1976},
  author = {T.L. Blundell and L.N. Johnson},
  address = {New York}
}

@ARTICLE{BROC76,
  author = {B. Brocklehurst},
  title = {Spin Correlation in the Geminate Recombination of Radical Ions in
	Hydrocarbons. {P}art 1.- {T}heory of the magnetic field effect},
  journal = {J.~Chem.~Soc.~Far.~Trans.~II},
  year = {1976},
  volume = {72},
  pages = {1869--1884}
}

@BOOK{FASM76,
  title = {Handbook of Biochemistry and Molecular Biology},
  publisher = {CRC Press},
  year = {1976},
  author = {Gerald D. Fasman and Herbet Alexander Sober},
  address = {New York}
}

@ARTICLE{GILL76,
  author = {D. T. Gillespie},
  title = {A General Method for Numerically Simulating the Stochastic Time Evolution
	of Coupled Chemical Reactions},
  journal = JCP,
  year = {1976},
  volume = {22},
  pages = {403--434},
  number = {4}
}

@ARTICLE{HARA76,
  author = {N. Haran and M. Shporer},
  title = {Study of Water Permeability through Phospholipid Vesicle Membranes
	by {$^{17}\!$O-NMR}},
  journal = {Biochim.~Biophys.~Acta},
  year = {1976},
  volume = {{\bf 462}},
  pages = {638--646},
  keywords = {liposomes, paramagnetic contrast agents}
}

@ARTICLE{HESK76,
  author = {T.R. Hesketh and G.A. Smith and M.D. Houslay and K.A. McGill and
	N.J.M. Birdsall and J. Metcalfe and G.B. Waren},
  title = {Annular lipids determine the ATPase activity of a Calcium transport
	protein complexed with dipalmitoyllecithin},
  journal = BCH,
  year = {1976},
  volume = {15},
  pages = {4145--4151}
}

@ARTICLE{KABS76,
  author = {W. Kabsch},
  title = {A solution for the best rotation to relate two sets of vectors},
  journal = ACA,
  year = {1976},
  volume = {32},
  pages = {922--923}
}

@ARTICLE{LaGr76,
  author = {R. A. LaBudde and D. Greenspan},
  title = {Energy and Momentum Conserving Methods of Arbitrary Order for the
	Numerical Integration of Equations of Motion \mbox{II}. \mbox{M}otion
	of a System of Particles},
  journal = {Numer. Math.},
  year = {1976},
  volume = {26},
  pages = {1--16}
}

@ARTICLE{LaWa76,
  author = {J. D. Lambert and I. A. Watson},
  title = {Symmetric Multistep Methods for Periodic Initial Value Problems},
  journal = {J. Inst.\ Math.\ Applics.},
  year = {1976},
  volume = {18},
  pages = {189--202}
}

@ARTICLE{LATO76,
  author = {R. Latorre and H. E. Hall},
  title = {Dipole potential measurements in assymetric membranes},
  journal = NAT,
  year = {1976},
  volume = {264},
  pages = {361--363},
  annote = {get ref}
}

@ARTICLE{Levi76,
  author = {M. Levitt},
  title = {A Simplified Representation of Protein Conformations for Rapid Simulation
	of Protein Folding},
  journal = {J. Molec.\ Bio.},
  year = {1976},
  volume = {104},
  pages = {59--107}
}

@ARTICLE{MAFF76,
  author = {L. Maffei and A. Fiorentini},
  title = {The Unresponsive Regions of Visual Cortical Receptive Fields},
  journal = {Vis. Res.},
  year = {1976},
  volume = {16},
  pages = {1131--1139}
}

@ARTICLE{MARC76,
  author = {S. Mar\v{c}elja and N. Radic},
  title = {Repulsion of Interfaces Due to Boundary Water},
  journal = CPL,
  year = {1976},
  volume = {42},
  pages = {129--130},
  number = {1},
  annote = {exponential bilayer repulsion; water structure modification; bound
	(frozen) water; Landau expansion of free energy}
}

@BOOK{McQu76,
  title = {Statistical Mechanics},
  publisher = {Harper and Row},
  year = {1976},
  author = {D. A. McQuarrie},
  address = {New York}
}

@ARTICLE{METT76,
  author = {R.L. van Metter and R.S. Knox},
  title = {On the relation between absorption and emission spectra of molecules
	in solution},
  journal = {Chem.~Phys.},
  year = {1976},
  volume = {12},
  pages = {333--340}
}

@ARTICLE{MITC76,
  author = {P. Mitchell},
  title = {Possible Molecular Mechanisms of the Protonmotive Function of Cytochrome
	Systems},
  journal = {J.\ Theor.\ Biol.},
  year = {1976},
  volume = {62},
  pages = {327--367},
  annote = {original Q-cycle mechanism}
}

@ARTICLE{NAND76,
  author = {Pradip K.\ Nandi},
  title = {Thermodynamic Parameters of Transfer of N-Acetyl Esters of Different
	Amino Acids from Organic Solvents to Water},
  journal = {Int.\ J.\ Pept.\ Prot.\ Res.},
  year = {1976},
  volume = {8},
  pages = {253--264}
}

@ARTICLE{OEST76,
  author = {Oesterhelt, D.},
  title = {Bacteriorhodopsin as an example of a light-driven proton pump},
  journal = {Angew.\ Chem.},
  year = {1976},
  volume = {15},
  pages = {16--24}
}

@ARTICLE{POTT76,
  author = {J.D. Potter and J.C. Seidel and P. Leavis and S.S. Lehrer and J.
	Gergely},
  title = {Effect of {Ca}$^{2+}$ binding on troponin {C}. {C}hanges in spin
	label mobility, extrinsic fluorescence, and sulfhydryl reactivity},
  journal = {J. Biol. Chem.},
  year = {1976},
  volume = {251},
  pages = {7551--6}
}

@ARTICLE{RECO76,
  author = {M.~T.~Record and T.~M~Lohman and P.~DeHaseth},
  title = {Ion effects on ligand-nucleic acid interactions},
  journal = JMB,
  year = {1976},
  volume = {107},
  pages = {145--158},
  annote = {taken from MURD91}
}

@ARTICLE{ROBS76,
  author = {B. Robson and E. Suzuki},
  title = {Conformational Properties of Amino Acid Residues in Globular Proteins},
  journal = JMB,
  year = {1976},
  volume = {107},
  pages = {327}
}

@ARTICLE{ROSS76,
  author = {Michael G. Rossman and Patrick Argos},
  title = {Exploring Structural Homology of Proteins},
  journal = JMB,
  year = {1976},
  volume = {105},
  pages = {75--95}
}

@ARTICLE{SCHU76A,
  author = {Klaus Schulten and Roy G. Gordon},
  title = {Quantum Theory of Angular Momentum Coupling in Reactive Collisions},
  journal = JCP,
  year = {1976},
  volume = {64},
  pages = {2918--2938}
}

@ARTICLE{SCHU76B,
  author = {Klaus Schulten and Roy G. Gordon},
  title = {Recursive Evaluation of $3j$- and $6j$-Coefficients},
  journal = CPC,
  year = {1976},
  volume = {11},
  pages = {269--278}
}

@ARTICLE{SCHU76,
  author = {Klaus Schulten and I. Ohmine and Martin Karplus},
  title = {Correlation Effects in the Spectra of Polyenes},
  journal = JCP,
  year = {1976},
  volume = {64},
  pages = {4422--4441}
}

@ARTICLE{SCHU76C,
  author = {Klaus Schulten and H. Staerk and Albert Weller and Hans-Joachim Werner
	and B. Nickel},
  title = {Magnetic Field Dependence of the Geminate Recombination of Radical
	Ion Pairs in Polar Solvents},
  journal = ZPC,
  year = {1976},
  volume = {NF101},
  pages = {371--390}
}

@ARTICLE{SONG76,
  author = {P-S. Song and P. Koka and B.B. Prezelin and F.T. Haxo},
  title = {Molecular topology of the photosynthetic light-harvesting pigment
	complex, peridinin-chloroophyll a-protein, from marine dinoflagellates},
  journal = BC,
  year = {1976},
  volume = {15},
  pages = {4422--4427}
}

@ARTICLE{WARS76,
  author = {A. Warshel},
  title = {Bicycle-pedal model for the first step in the vision process.},
  journal = NAT,
  year = {1976},
  volume = {260},
  pages = {679--683}
}

@ARTICLE{WARS76A,
  author = {A. Warshel and M. Levitt},
  title = {Theoretical Studies of Enzymatic Reactions: Dielectric, Electrostatic
	and Steric Stabilization of the Carbonium Ion in the Reaction of
	Lysozyme.},
  journal = JMB,
  year = {1976},
  volume = {103},
  pages = {227--249}
}

@ARTICLE{WILL76,
  author = {D.~J. Willshaw and C. von der Malsburg},
  title = {How Patterned Neural Connections can be set up by Self-organization},
  journal = {Proc. R. Soc. Lond.},
  year = {1976},
  volume = {B194},
  pages = {431--445}
}

@ARTICLE{AUST75,
  author = {R. H. Austin and K. W. Beeson adn L. Eisenstein and H. Frauenfelder
	and I. C. Gunsalus},
  title = {FIXME},
  journal = BCH,
  year = {1975},
  volume = {14},
  pages = {5355}
}

@ARTICLE{BAKE75,
  author = {H. Nordean Baker and Gotto, Jr., Antonio M. and Richard L. Jackson},
  title = {The Primary Structure of Human Plasma High Density Apolipoprotein
	Glutamine {I} ({ApoA-I})},
  journal = JBC,
  year = {1975},
  volume = {250},
  pages = {2725--2738}
}

@ARTICLE{BALD75,
  author = {Robert L. Baldwin},
  title = {Intermediates in Protein Folding and the Mechanism of Protein Folding},
  journal = ARB,
  year = {1975},
  volume = {44},
  pages = {453}
}

@ARTICLE{BAWI75,
  author = {S. W. Bawin and L. K. Kaczmarek and W. R. Adey},
  title = {Effects of Modulated VHF Fields on the Central Nervous System},
  journal = {Annals of the New York Academy of Sciences},
  year = {1975},
  volume = {247},
  pages = {74--81}
}

@ARTICLE{BIRG75,
  author = {Robert R. Birge and Klaus Schulten and Martin Karplus},
  title = {Possible Influence of a Low-Lying ``Covalent'' Excited State on the
	Absorption Spectrum and Photoisomerization of 11-cis Retinal},
  journal = CPL,
  year = {1975},
  volume = {31},
  pages = {451--454},
  number = {3}
}

@ARTICLE{BoKL75,
  author = {A.B. Bortz and M.H. Kalos and J.L. Lebowitz},
  title = {A new algorithm for {M}onte {C}arlo simulation of {I}sing spin systems},
  journal = JCP,
  year = {1975},
  volume = {17},
  pages = {10}
}

@INCOLLECTION{Dahl75,
  author = {G. Dahlquist},
  title = {Error Analysis for a Class of Methods for Stiff Nonlinear Initial
	Value Problems},
  booktitle = {Numerical Analysis, Dundee 1975},
  publisher = {Springer-Verlag},
  year = {1975},
  editor = {G. A. Watson},
  pages = {60--74},
  address = {Berlin},
  nremark = {cited on p.~156 of SaCa94}
}

@ARTICLE{DEIS75,
  author = {J. Deisenhofer and W. Steigemann},
  title = {Crystallographic Refinement of the Structure of Bovine Pancreatic
	Trypsin Inhibitor at 1.5 {{ \AA}} Resolution},
  journal = ACB,
  year = {1975},
  volume = {31},
  pages = {238}
}

@INBOOK{GILB75,
  title = {Protein-Ligand Interactions},
  publisher = {de Gruyter},
  year = {1975},
  editor = {H. Sund and G. Bauer},
  author = {W. Gilbert},
  address = {Berlin}
}

@ARTICLE{GREE75,
  author = {N. M. Green},
  title = {Avidin},
  journal = {Advan. Prot. Chem.},
  year = {1975},
  volume = {29},
  pages = {85--133},
  annote = {june 1}
}

@ARTICLE{HEND75,
  author = {R. Henderson and P. N. T. Unwin},
  title = {Three-Dimensional Model of Purple Membrane Obtained by Electron Microscopy},
  journal = NAT,
  year = {1975},
  volume = {257},
  pages = {28--32}
}

@ARTICLE{HEYN75,
  author = {M. P. Heyn and P. J. Bauer and N. A. Dencher},
  title = {A Natural {CD} Label to Probe the Structure of the Purple Membrane
	From {{\em Halobacterium halobium}} by Means of Exciton Coupling
	Effects},
  journal = BBRC,
  year = {1975},
  volume = {67},
  pages = {897--903}
}

@BOOK{KERN75,
  title = {Ratfor - A Preprocessor For A Rational Fortran},
  publisher = {Bell Laboratories},
  year = {1975},
  author = {B.~W. Kernighan},
  address = {Murray Hill}
}

@ARTICLE{LEVI75,
  author = {M. Levitt and A. Warshel},
  title = {Computer simulation of protein folding},
  journal = NAT,
  year = {1975},
  volume = {253},
  pages = {694--698}
}

@ARTICLE{Lewi75,
  author = {J. H. Lewis},
  title = {Fate maps and the pattern of cell division: a calculation for the
	chick wing-bud},
  journal = {Journal of Embryology and Experimental Morphogenesis},
  year = {1975},
  volume = {33},
  pages = {419--434},
  number = {2}
}

@ARTICLE{LOZI75,
  author = {Lozier, R. H. and Bogomolni, R. A. and Stoeckenius, W.},
  title = {Bacteriorhodopsin: A Light-Driven Proton Pump in {{\em Halobacterium
	halobium}}},
  journal = BJ,
  year = {1975},
  volume = {15},
  pages = {955--962},
  annote = {title was CYCLE1}
}

@ARTICLE{MALP75,
  author = {J. Malpeli and F. H. Baker},
  title = {The Representation of the Visual Field in the Lateral Geniculate
	Nucleus of {\em Macaca mulatta}},
  journal = JCN,
  year = {1975},
  volume = {161},
  pages = {569--594}
}

@ARTICLE{MMBS75,
  author = {F. Momany and R. McGuire and A. Burgess and H. Scheraga},
  title = {Energy Parameters in Polypeptides VII},
  journal = {J. Chem.\ Phys.},
  year = {1975},
  volume = {79},
  pages = {2361--2381}
}

@ARTICLE{PtRa75,
  author = {O. B. Ptitsyn and A. A. Rashin},
  title = {A Model of Myoglobin Self-Organization},
  journal = BPC,
  year = {1975},
  pages = {1--20},
  number = {1}
}

@INCOLLECTION{SAUE75,
  author = {K. Sauer},
  title = {Primary Events and the Trapping of Energy},
  booktitle = {Bioenergetics of Photosynthesis},
  publisher = {Academic Press},
  year = {1975},
  editor = {Govindjee},
  pages = {115--181},
  addresses = {New York}
}

@ARTICLE{SCHE75,
  author = {K. L. Schepler and W. R. Dunham and R. H. Sands and J. A. Fee and
	R. H. Abeles},
  title = {A Physical Explanation of the EPR Spectrum Observed During Catalysis
	by Enzymes Utilizing Coenzyme B$_{12}$},
  journal = BBA,
  year = {1975},
  volume = {397},
  pages = {510--518}
}

@ARTICLE{SCHI75,
  author = {Hansgeorg Schindler and Joachim Seelig},
  title = {Deuterium Order Parameters in Relation to Thermodynamic Properties
	of a Phospholipid Bilayer. A Statistical Mechanical Interpretation},
  journal = BCH,
  year = {1975},
  volume = {14},
  pages = {2283--2287},
  number = {11},
  annote = {surface tension for soaps \gamma=18\ldots20 dynes/cm; gives a more
	detailed definition of S_{\rm mol} and S_{\rm CD} and their relationship
	which is not always S_{\rm mol} = -2 S_{\rm mol}, only for axially
	symmetric segment motion},
  keywords = {theory; DPPC; phase transition; thickness; trans/gauche/kink/jog;
	Mar\v{c}elja}
}

@ARTICLE{SCHU75,
  author = {Klaus Schulten and Roy G. Gordon},
  title = {Exact Recursive Evaluation of $3j$- and $6j$-Coefficients for Quantum-Mechanical
	Coupling of Angular Momenta},
  journal = JMP,
  year = {1975},
  volume = {16},
  pages = {1961--1970}
}

@ARTICLE{SCHU75A,
  author = {Klaus Schulten and Roy G. Gordon},
  title = {Semiclassical Approximation to $3j$- and $6j$-Coefficients for Quantum-Mechanical
	Coupling of Angular Momenta},
  journal = JMP,
  year = {1975},
  volume = {16},
  pages = {1971--1988}
}

@BOOK{STRY75,
  title = {Biochemistry},
  publisher = {W. H. Freeman and Comp.},
  year = {1975},
  author = {Lubert Stryer},
  address = {New York},
  edition = {3}
}

@ARTICLE{TALL75,
  author = {A.R. Tall and D.M. Small and G.G. Shipley and R.S. Lees},
  title = {Apoprotein Stability and Lipid-protein Interactions in Human Plasma
	High Density Lipoproteins},
  journal = {Proc. Natl. Acad. Sci. U.S.A.},
  year = {1975},
  volume = {72},
  pages = {4940}
}

@ARTICLE{AMZE74,
  author = {L. M. Amzel and R. J. Poljak and F. Saul and J. M. Varga and F. F.
	Richard},
  title = {Electrostatics in Biomolecular Structure and Dynamics},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1974},
  volume = {71},
  pages = {1427}
}

@ARTICLE{CIZE74,
  author = {J. Cizek and J. Paldus and I. Hubac},
  title = {Correlation Effects in the Low-Lying Excited States of PPP Models
	of Alternant Hydrocarbons. I. Qualitative Rules for the Effect of
	Limited Configuration Interaction},
  journal = IJQC,
  year = {1974},
  volume = {8},
  pages = {951--970}
}

@ARTICLE{CREI74,
  author = {T. E. Creighton},
  title = {Intermediates in the Refolding of Reduced Pancreatic Trypsin Inhibitor},
  journal = JMB,
  year = {1974},
  volume = {87},
  pages = {579--602}
}

@ARTICLE{CREI80,
  author = {T. E. Creighton},
  title = {Role of the Environment in the Refolding of Reduced Pancreatic Trypsin
	Inhibitor},
  journal = JMB,
  year = {1974},
  volume = {144},
  pages = {512--550}
}

@ARTICLE{DIAM74,
  author = {J. M. Diamond and Y. Katz},
  title = {Interpretation of nonelectrolyte partition coefficients between dimyristoyl
	lecithin and water},
  journal = {J. Membrane Biol.},
  year = {1974},
  volume = {17},
  pages = {121--154},
  annote = {Nonelectrolyte partition coefficient and free energies of solution
	in dimyristoyl lecithin liposomes and in bulk nonpolar solvents were
	compared. Individual substituent groups tend to have consistent effects
	on K, permitting the extraction of incremental free energies, enthalpies,
	and entropies of partition and of solution. Values of the selectivity
	constant and of free energy for the -CH2 and -OH groups in lecithin
	suggest that partitioned solutes are mainly located in a region slightly
	less hydrophobic than octanol and similar to C5H11OH in its solvent
	properties. Lecithin discriminates branched solute more than does
	a bulk solvent with the same s value. Below the phase transition
	temperature, $\delta$S and $\delta$H of partition increase 10 fold,
	and change sign from minus to plus. Resistance of nonelctrolyte permeation
	is inhomogeneously distributed through the bilayer, region of maximum
	partition does not provide the rate-limiting barrier. An appendix
	is given which derives the relation of permeability with local partition
	coefficient and local diffusion constant. This is the fourth paper
	of a series. Maybe get other 3 too.}
}

@BOOK{GASI74,
  title = {Quantum Physics},
  publisher = {John Wiley \& Sons},
  year = {1974},
  author = {Stephen Gasiorowicz},
  address = {New York, Chichester, Brisbane, Toronto, Singapore}
}

@ARTICLE{GWIN74,
  author = {E. Gwinner},
  title = {Endogenous temporal control of migratory restlessness in warblers},
  journal = {Naturwiss.},
  year = {1974},
  volume = {61},
  pages = {405}
}

@ARTICLE{HAY74,
  author = {P. Hay and I. Shavitt},
  title = {{\it Ab initio} Configuration Interaction Studies of the {\it pi}-{Electron}
	State of Benzene.},
  journal = JCP,
  year = {1974},
  volume = {60},
  pages = {2865}
}

@ARTICLE{HITC74,
  author = {P. B. Hitchcock and R. Mason and K. M. Thomas and G. G. Shipley},
  title = {Structural chemistry of 1,2-dilauroyl-DL-phosphatidylethanolamine:
	Molecular conformation and intermolecular packing of phospholipids},
  journal = PNAS,
  year = {1974},
  volume = {71},
  pages = {3036--3040},
  annote = {requested Tx=19920908.}
}

@ARTICLE{HOPF74,
  author = {J. J. Hopfield},
  title = {Electron transfer between biological molecules by thermally activated
	tunneling},
  journal = PNAS,
  year = {1974},
  volume = {71},
  pages = {3640--3644}
}

@ARTICLE{HUBE74,
  author = {D.~Hubel and T.~N. Wiesel},
  title = {Sequence regularity and geometry of orientation columns in monkey
	striate cortex},
  journal = JCN,
  year = {1974},
  volume = {158},
  pages = {267--293}
}

@ARTICLE{IVAN74,
  author = {V.~I.~Ivanov and L.~E.~Minchenkova and M.~D.~Frank-Kamentskii and
	A.~K.~Schyolkina.},
  title = {The {B} to {A} transition of {DNA} in solution},
  journal = JMB,
  year = {1974},
  volume = {87},
  pages = {817--833}
}

@ARTICLE{OPDE74,
  author = {J.A.F. Op den Kamp and J. de Gier and L.L.M. van Deenen},
  title = {Cobra venom phospholipase {A$_2$}: a review of its action toward
	lipid/water interfaces},
  journal = BBA,
  year = {1974},
  volume = {345},
  pages = {253--256}
}

@ARTICLE{LANG74,
  author = {S. Langhoff and E. Davidson},
  title = {Configuration Interaction Calculations on the Nitrigen Molecule.},
  journal = IJQC,
  year = {1974},
  volume = {8},
  pages = {61}
}

@ARTICLE{MARC74,
  author = {S. Mar\v{c}elja},
  title = {Chain ordering in liquid crystals},
  journal = BBA,
  year = {1974},
  volume = {367},
  pages = {165--176},
  annote = {experimental techniques: X-ray, NMR, ESR, calorimetry, transport
	studies (and I include photobleaching, QENS [neutron scattering],
	STM [scanning tunneling microscopy], AFM [atomic force microscopy],);
	molecular field model not good close to transition temperature as
	it does neglect fluctuations; molecular field is self-consistent
	approximation; gives relation between lateral pressure and area per
	head group; area per head group for PCs in LC phase typically 60...70\AA^2;
	lateral pressure 25 dynes/cm; very substantial paper},
  keywords = {theory; molecular field; lateral presure; order parameters; gauche
	fraction; cholesterol},
  suggestions = {also study lateral pressure in gel phase}
}

@ARTICLE{MISI74,
  author = {R. L. Misiorowski and M. A. Wells},
  title = {The activity of phospholipase {A}$_2$ in reversed micelles of phosphotidylcholine
	in diethyl ether: effect of water and cations},
  journal = BCH,
  year = {1974},
  volume = {13},
  pages = {4921--4927},
  annote = {get it, paper on dehydration}
}

@ARTICLE{NOLL74,
  author = {M.~Noll},
  title = {Subunit structure of chromatin},
  journal = NAR,
  year = {1974},
  volume = {1},
  pages = {1573--1578},
  annote = {over 80\% of nuclear {DNA}is organized in nucleosomes}
}

@ARTICLE{OEST74a,
  author = {Dieter Oesterhelt and Lieselotte Schumann},
  title = {Reconstitution of Bacteriorhodopsin},
  journal = FEBS,
  year = {1974},
  volume = {44},
  pages = {262--265}
}

@ARTICLE{OEST74,
  author = {Dieter Oesterhelt and Lieselotte Schumann and Hedwig Gruber},
  title = {Light-dependent Reaction of Bacteriorhodopsin with Hydroxylamine
	in Cell Suspensions of {\it {H}alobacterium halobium}: {D}emonstration
	of an Apo-membrane},
  journal = FEBS,
  year = {1974},
  volume = {44},
  pages = {257--261}
}

@ARTICLE{PIET74,
  author = {W.A. Pierterson and J.C. Vidal and J.J. Volwerk and G.H. de Haas},
  title = {Zymogen-catalyzed hydrolysis of monomeric substrates and the presence
	of a recognition site for lipid-water interfaces in phospholipase
	{A$_2$}},
  journal = BCH,
  year = {1974},
  volume = {13},
  pages = {1455--1460},
  annote = {classical paper on PLA2 zymogen comparison}
}

@ARTICLE{PRIV74,
  author = {P.\ L.\ Privalov and N.\ N.\ Khechinashvili},
  title = {A Thermodynamic Approach to the Problem of Stabilization of Globular
	Protein Structure: A Calorimetric Study},
  journal = JMB,
  year = {1974},
  volume = {86},
  pages = {665--684}
}

@ARTICLE{RACK74,
  author = {Racker, E. and Stoeckenius, W.},
  title = {Reconstitution of Purple Membrane Vesicles Catalyzing Light-driven
	Proton Uptake and Adenosine Triphosphate Formation},
  journal = JBC,
  year = {1974},
  volume = {249},
  pages = {662--663}
}

@ARTICLE{RICH74,
  author = {F.\ M.\ Richards},
  title = {The Interpretation of Protein Structures: Total Volume, Group Volume
	Distributions and Packing Density},
  journal = JMB,
  year = {1974},
  volume = {82},
  pages = {1--14}
}

@ARTICLE{SEEL74a,
  author = {Anna Seelig and Joachim Seelig},
  title = {The Dynamic Structure of Fatty Acyl Chains in a Phospholipid Bilayer
	Measured by Deuterium Magnetic Resonance},
  journal = BCH,
  year = {1974},
  volume = {13},
  pages = {4839--4845},
  number = {23},
  annote = {the two chains are not equivalent; S_mol=0.45 \@ T=41^oC; 3...6 gauche
	per chain; S_mol = -2S_CD = 1/2 <3cos^2\theta -1>; 41^o C is the
	main phase transition point gel/LC for DPPC},
  keywords = {experimenta; DPPC; membrane; L_\alpha; order parameter plateau region},
  suggestions = {look at trans/gauche/kink distribution; look at S_z: anisotropy of
	motion; give average thickness data (P-P); thesis: show ray traced
	picture of one lipid (#49?) from the end of the simulatoion, in color
	(in stereo?)}
}

@ARTICLE{SEEL74,
  author = {Seeling, J. and Niederberger, W.},
  title = {Two Pictures of a Lipid Bilayer. \ {A} Comparison between Deuterium
	Label and Spin Label Experiments},
  journal = {Biochemistry, N. Y.},
  year = {1974},
  volume = {I3},
  pages = {1585--1588}
}

@BOOK{Vara74,
  title = {{L}ie groups, {L}ie algebras and their representation},
  publisher = {Prentice-Hall},
  year = {1974},
  author = {V. S. Varadarajan},
  address = {Englewood-Cliffs, NJ}
}

@ARTICLE{WaHy74,
  author = {R. F. Warming and B. J. Hyett},
  title = {The modified equation approach to the stability and accuracy analysis
	of finite difference methods},
  journal = { J.~Comput.\ Phys},
  year = {1974},
  volume = {14},
  pages = {159--179}
}

@ARTICLE{WARS74,
  author = {A. Warshel and M. Karplus},
  title = {Calculation of {$\pi \pi ^*$} Excited State Conformations and Vibronic
	Structure of Retinal and Related Molecules.},
  journal = JACS,
  year = {1974},
  volume = {96},
  pages = {5677--5689}
}

@ARTICLE{WILT74,
  author = {W. Wiltschko},
  title = {Der {M}agnetkompass der {G}artengra\ss m\"{u}cke ({\em Sylvia borin})},
  journal = {J.~Ornithol.},
  year = {1974},
  volume = {115},
  pages = {1--7}
}

@ARTICLE{AhCo73,
  author = {A. Ahmad and L. Cohen},
  title = {A numerical integration scheme for the $N$-body gravitational problem},
  journal = {J. Comput. Phys.},
  year = {1973},
  volume = {12},
  pages = {389--402}
}

@ARTICLE{AHMA73,
  author = {A. Ahmad and L. Cohen},
  title = {A Numerical Integration Scheme for the {N}-Body Gravitational Problem},
  journal = JCMP,
  year = {1973},
  volume = {12},
  pages = {389--402},
  annote = {early distance class scheme with 2 classes; adaptive time step; they
	do some error analysis but do not find a conclusive measure},
  keywords = {astrophysics; algorithm}
}

@ARTICLE{Anfi73,
  author = {C. Anfinsen},
  title = {Principles that Govern the Folding of Protein Chains},
  journal = SCI,
  year = {1973},
  volume = {181},
  pages = {223--230}
}

@ARTICLE{ARMS73,
  author = {C. M. Armstrong and F. Bezanilla},
  title = {FIXME},
  journal = NAT,
  year = {1973},
  volume = {242},
  pages = {459--461}
}

@BOOK{BAYM73,
  title = {Lectures on Quantum Mechanics},
  publisher = {W. A. Benjamin, Inc.},
  year = {1973},
  author = {G. Baym},
  address = {Reading, Massachusetts}
}

@ARTICLE{CADE73,
  author = {D.A. Cadenhead and F, Muller--Landau},
  title = {Pure and mixed monomolecular films of 12-nitroxide stearate},
  journal = BBA,
  year = {1973},
  volume = {307},
  pages = {279}
}

@INPROCEEDINGS{HERT73,
  author = {H. G. Hertz},
  title = {Nuclear Magnetic Relaxation Spectroscopy},
  booktitle = {Water: A Comprehensive Treatise (Vol. 3)},
  year = {1973},
  editor = {F. Franks},
  address = {New York},
  publisher = {Plenum Press},
  chapter = {7}
}

@ARTICLE{HUDS73,
  author = {B. Hudson and B.E. Kohler},
  title = {Polyene spectroscopy: The lowest lying energy excited singlet state
	of diphenyloctatraene and other linear polyenes},
  journal = JCP,
  year = {1973},
  volume = {59},
  pages = {4984--5002}
}

@ARTICLE{KRET73,
  author = {R. H. Kretsinger and C. E. Nockolds},
  title = {Carp Muscle Calcium-binding Protein: {II}. {Structure} determination
	and general description},
  journal = JBC,
  year = {1973},
  volume = {248},
  pages = {3313--3326}
}

@ARTICLE{LIN73,
  author = {S. Lin and B. W. Kernighan},
  title = {An Effective Heuristic Algorithm for the Travelling Salesman Problem},
  journal = {Operations Research},
  year = {1973},
  volume = {21},
  pages = {498--516}
}

@ARTICLE{MALS73,
  author = {C. von der Malsburg},
  title = {Self-organization of Orientation Sensitive Cells in the Striate Cortex},
  journal = {Kybernetik},
  year = {1973},
  volume = {14},
  pages = {85--100}
}

@ARTICLE{MARC73,
  author = {S. Mar\v{c}elja},
  title = {Molecular Model for Phase Transitions in Biological Membranes},
  journal = NAT,
  year = {1973},
  volume = {241},
  pages = {451--453},
  annote = {good introduction},
  keywords = {membrane; phase transition; order parameter; molecular field model}
}

@ARTICLE{MEAK73,
  author = {P. Meakin and J. P. Jesson},
  title = {Computer Simulation of Multipulse and {Fourier} Transform NMR Experiments.
	I. Simulations Using the Bloch Equations},
  journal = {Journal of Magnetic Resonance},
  year = {1973},
  volume = {10},
  pages = {290--315}
}

@BOOK{Mose73,
  title = {Stable and Random Motions in Dynamical Systems},
  publisher = {Princeton University Press},
  year = {1973},
  author = {J{\"u}rgen Moser},
  address = {Princeton, New Jersey},
  nremark = {CALL NO: 521.1M853s}
}

@ARTICLE{OEST73a,
  author = {Dieter Oesterhelt and Marion Meentzen and Lieslotte Schumann},
  title = {Reversible Dissociation of the Purple Complex in Bacteriorhodopsin
	and Identification of 13-{\it cis} and all-{\it trans} Retinal as
	its Chromophores},
  journal = EJB,
  year = {1973},
  volume = {40},
  pages = {453--463}
}

@ARTICLE{OEST73,
  author = {Oesterhelt, D. and Stoeckenius, W.},
  title = {Functions of a New Photoreceptor Membrane},
  journal = PNAS,
  year = {1973},
  volume = {70},
  pages = {2853--2857}
}

@ARTICLE{PILB73,
  author = {J. R. Pilbrow and M. E. Winfield},
  title = {Computer Simulation of Low Symmetry E.S.R. Spectra due to Vitamin
	B$_{12r}$ and Model Systems},
  journal = MP,
  year = {1973},
  volume = {25},
  pages = {1073}
}

@ARTICLE{PODO73,
  author = {R. J. Podolsky and C. Nolan},
  title = {Muscle contraction transients, cross-bridge kinetics, and the Fenn
	effect},
  journal = {Cold Spring Harb. Symp. Quant. Biol.},
  year = {1973},
  volume = {37},
  pages = {661}
}

@ARTICLE{RAO73,
  author = {S. T. Rao and Michael G. Rossman},
  title = {Comparison of Super-Secondary Structures in Proteins},
  journal = JMB,
  year = {1973},
  volume = {76},
  pages = {241--256}
}

@ARTICLE{RIDL73,
  author = {J. Ridley and M. Zerner},
  title = {An INDO Technique for Spectroscopy: Pyrrole and the Azines},
  journal = TCA,
  year = {1973},
  volume = {32},
  pages = {111--134}
}

@TECHREPORT{Take73,
  author = {F.~Takens},
  title = {Introduction to Global Analysis},
  institution = {Rijksuniversiteit Utrecht},
  year = {1973},
  number = {Commun. Math. Inst., Vol.~2}
}

@ARTICLE{VERG73,
  author = {R. Verger and M.C.E. Mieras and G.H. de Haas},
  title = {Action of phospholipase {A} at interfaces},
  journal = JBC,
  year = {1973},
  volume = {248},
  pages = {4023--4034}
}

@ARTICLE{AaSi72,
  author = {J. Aagaard and W.R. Sistrom},
  title = {Control of synthesis of reaction center bacteriochlorophyll in photosynthetic
	bacteria},
  journal = PCPB,
  year = {1972},
  volume = {15},
  pages = {209--225}
}

@ARTICLE{BEZA72,
  author = {F.~Bezanilla and C.~M.~Armstrong},
  title = {Negative conductance caused by entry of sodium and cesium ions into
	the potassium channels of squid axons},
  journal = JGP,
  year = {1972},
  volume = {60},
  pages = {588--608},
  annote = {first introduces the idea of the interaction between the ion and
	the carbonyl oxygen atoms}
}

@ARTICLE{CADE72,
  author = {D.A. Cadenhead and K.E. Bean},
  title = {Selected lipid monolayers on aqeous-glycerol and aqeous-urea substrates},
  journal = BBA,
  year = {1972},
  volume = {290},
  pages = {43--50}
}

@ARTICLE{CONL72,
  author = {T. Conlon and R. Outhred},
  title = {Water Diffusion Permeability of Erythrocytes Using an {NMR} Technique},
  journal = {Biochim.~Biophys.~Acta},
  year = {1972},
  volume = {{\bf 288}},
  pages = {354--361},
  keywords = {membranes}
}

@ARTICLE{Flyn72,
  author = {M. Flynn},
  title = {Some Computer Organizations and Their Effectiveness},
  journal = {IEEE Trans. Comput.},
  year = {1972},
  volume = {C},
  pages = {94},
  number = {21}
}

@ARTICLE{HAYD72,
  author = {D.A. Haydon and S.B. Hladky},
  title = {Ion transport across thin lipid membranes: a critical discussion
	of mechanisms in selected systems},
  journal = {Q. Rev. Biophys.},
  year = {1972},
  volume = {5},
  pages = {187--192}
}

@BOOK{Keet72,
  title = {Biological Science: Second Edition},
  publisher = {W.W. Norton and Company},
  year = {1972},
  author = {W. Keeton},
  address = {New York}
}

@ARTICLE{SCHU72,
  author = {Klaus Schulten and Martin Karplus},
  title = {On the Origin of a Low-Lying Forbidden Transition in Polyenes and
	Related Molecules},
  journal = CPL,
  year = {1972},
  volume = {14},
  pages = {305--309},
  number = {3},
  annote = {June 1}
}

@ARTICLE{SING72,
  author = {S.J. Singer and G.L. Nicolson},
  title = {The fluid mosaic model of the structure of cell membranes},
  journal = SCI,
  year = {1972},
  volume = {173},
  pages = {720--731}
}

@ARTICLE{SUUR72,
  author = {J. Suurkusk and I. Wadso},
  title = {Thermochemistry of the Avidin--Biotin Reaction},
  journal = EJB,
  year = {1972},
  volume = {28},
  pages = {438--441},
  annote = {june 1}
}

@ARTICLE{WEIS72,
  author = {C. Weiss},
  title = {The Pi electron structure and absorption spectra of chlorophylls
	in solution},
  journal = {J. Mol. Spectrosc. },
  year = {1972},
  volume = {44},
  pages = {37--80}
}

@ARTICLE{WILT72,
  author = {W. Wiltschko and R. Wiltschko},
  title = {Magnetic Compass of European robins},
  journal = SCI,
  year = {1972},
  volume = {176},
  pages = {62--64}
}

@ARTICLE{FULL71,
  author = {F. B. Fuller},
  title = {The writhing number of a space curve},
  journal = PNAS,
  year = {1971},
  volume = {68},
  pages = {815--819}
}

@BOOK{Gear71,
  title = {Numerical Initial Value Problems in Ordinary Differential Equations},
  publisher = {Prentice-Hall},
  year = {1971},
  author = {Gear, C. W.},
  address = {Englewood Cliffs, N.~J.}
}

@ARTICLE{LEE71,
  author = {B. Lee and F. M. Richards},
  title = {The Interpretation of Protein Structures: Estimation of Static Accessibility},
  journal = JMB,
  year = {1971},
  volume = {55},
  pages = {379--400}
}

@ARTICLE{Meye71,
  author = {K. R. Meyer},
  title = {Generic Stability Properties of Periodic Points},
  journal = {Trans.\ Amer.\ Math.\ Soc.},
  year = {1971},
  volume = {154},
  pages = {273--277},
  nremark = {510.6 AMS}
}

@ARTICLE{OEST71,
  author = {D. Oesterhelt and W. Stoeckenius},
  title = {Blue membrane formation at low {pH}},
  journal = NAT,
  year = {1971},
  volume = {233},
  pages = {149},
  annote = {title was BUE1}
}

@ARTICLE{OEST71A,
  author = {D. Oesterhelt and W. Stoeckenius},
  title = {Rhodopsin-Like Protein From the Purple Membrane of {{\em Halobacterium
	halobium}}},
  journal = NATNB,
  year = {1971},
  volume = {233},
  pages = {149--152}
}

@ARTICLE{PALT71,
  author = {F. Paltauf and H. Hauser and M.C. Phillips},
  title = {Monolayer characteristics of some 1,2-diacyl,1-alkyl-2-acyl and 1,2-dialkyl
	phospholipids at the air-water interface},
  journal = BBA,
  year = {1971},
  volume = {249},
  pages = {539--547}
}

@ARTICLE{RAHM71,
  author = {A. Rahman and F. H. Stillinger},
  title = {Molecular Dynamics Study of Liquid Water},
  journal = JCP,
  year = {1971},
  volume = {55},
  pages = {3336--3359}
}

@BOOK{SiMo71,
  title = {Lectures on Celestial Mechanics},
  publisher = {Springer-Verlag},
  year = {1971},
  author = {C. L. Siegel and J. K. Moser},
  city = {Berlin},
  nremark = {521SI1VEK1971}
}

@ARTICLE{TRAU71,
  author = {H. Tr{\"a}uble},
  title = {The movement of molecules across lipid membranes: {A} molecular theory},
  journal = {J. Membrane Biol.},
  year = {1971},
  volume = {4},
  pages = {194--208},
  annote = {THE reference for dynamic kink theory of small molecule transport
	through membrane. Permeability of water calculated and comparable
	to experimental value.}
}

@ARTICLE{TULL71,
  author = {John C. Tully and Richard K. Preston},
  title = {Trajectory surface hopping approach to nonadiabatic molecular collision:
	{T}he reaction of {H$^{+}$} with {D$_{2}$}},
  journal = JCP,
  year = {1971},
  volume = {55},
  pages = {562--572}
}

@BOOK{ZIEN71,
  title = {The Finite Element Method in Engineering Science},
  publisher = {McGraw-Hill},
  year = {1971},
  author = {O.C. Zienkiewicz},
  address = {London}
}

@ARTICLE{ENGL70,
  author = {R. Englman and J. Jortner},
  title = {The energy gap law for radiationless transitions in large molecules},
  journal = {Mol.~Phys.},
  year = {1970},
  volume = {18},
  pages = {145--164}
}

@ARTICLE{FREE70,
  author = {S. T. Freer and J. Kraut and J. D. Robertus and H. T. Wright and
	Ng. H. Xuong},
  title = {Chymotrypsinogen: 2.5-{{\AA}} Crystal Structure, Comparison with
	$\alpha$-Chymotrypsin, and Implications for Zymogen Activation},
  journal = BCH,
  year = {1970},
  volume = {9},
  pages = {1997--2009}
}

@ARTICLE{Hast70,
  author = {W. K. Hastings},
  title = {{M}onte {C}arlo Sampling Methods Using {M}arkov Chains and their
	Applications},
  journal = {Biometrika},
  year = {1970},
  volume = {57},
  pages = {97--109},
  abstract = {Generalizes the Metropolis algorithm, and discusses its use for statistical
	problems. Includes discussion of error estimation, and of the use
	of a {M}arkov chain method as an importance sampler.}
}

@ARTICLE{LEBL70,
  author = {O.H.Jr. Le{B}lanc},
  title = {Single ion conductances in lipid bilayers},
  journal = BJ,
  year = {1970},
  volume = {14},
  pages = {94a. (Abstr.)}
}

@ARTICLE{Meye70,
  author = {K. R. Meyer},
  title = {Generic Bifurcation of Periodic Points},
  journal = {Trans.\ Amer.\ Math.\ Soc.},
  year = {1970},
  volume = {149},
  pages = {95--107},
  nremark = {510.6 AMS}
}

@BOOK{OrRh70,
  title = {Iterative Solution of Nonlinear Equations in Several Variables},
  publisher = {Academic Press},
  year = {1970},
  author = {J. M. Ortega and W. C. Rheinboldt},
  address = {New York}
}

@BOOK{WOOD70,
  title = {The Conservation of Orbital Symmetry},
  publisher = {Verlag Chemie},
  year = {1970},
  author = {Woodward, R B and Hoffmann R},
  address = {Weinheim/Deerfield Beach}
}

@INCOLLECTION{Butc69,
  author = {J. C. Butcher},
  title = {The Effective Order of {R}unge--{K}utta Methods},
  booktitle = {Conference on the Numerical Solution of Differential Equations, Lecture
	Notes in Mathematics},
  publisher = {Springer-Verlag},
  year = {1969},
  editor = {A. Dold and Z. Heidelberg and B. Eckmann},
  volume = {109},
  pages = {133--139},
  address = {New York}
}

@ARTICLE{DEWA68,
  author = {M. J. S. Dewar and T. Morita},
  title = {Ground States of Conjugated Molecules. XII. Improved Calculations
	for Compounds Containing Nitrogen and Oxygen.},
  journal = JACS,
  year = {1969},
  volume = {91},
  pages = {796--801},
  number = {4}
}

@BOOK{EISE69,
  title = {The Structure and Properties of Water},
  publisher = {Oxford University Press},
  year = {1969},
  author = {D. Eisenberg and W. Kauzmann},
  address = {Oxford}
}

@ARTICLE{KUBO69,
  author = {R. Kubo},
  title = {A stochastic theory of lineshape},
  journal = {Adv.~Chem.~Phys.},
  year = {1969},
  volume = {15},
  pages = {101--127}
}

@ARTICLE{LIEB69,
  author = {Ye. A. Liberman and V.P. Toplay},
  title = {Permeability of biomolecular phospholipid membranes for fat-soluble
	ions},
  journal = {Biophysics},
  year = {1969},
  volume = {14},
  pages = {477--487}
}

@ARTICLE{SCAN69,
  author = {A. Scanu and J. Toth and C. Edelstein and S. Koga and E. Stiller},
  title = {Fractionation of Human Serum High Density Lipoprotein in Urea Solutions.
	{E}vidence for Polypeptide Heterogeniety},
  journal = {Biochemistry},
  year = {1969},
  volume = {8},
  pages = {3309}
}

@ARTICLE{WHIT69,
  author = {J.~H.~White},
  title = {Self-linking and the Gauss integral in higher dimensions},
  journal = {Am.~J.~Math.},
  year = {1969},
  volume = {91},
  pages = {693--728},
  annote = {this is the original ref to Lk = wr + tw applied to DNA}
}

@ARTICLE{BROC68,
  author = {H. Brockerhoff},
  title = {Substrate specificity of pancreatic lipase},
  journal = BBA,
  year = {1968},
  volume = {159},
  pages = {296--303},
  annote = {get it, first paper on dehydration}
}

@ARTICLE{DEHA68,
  author = {G.H. De Hass and N.M. Postema and W. Nieuwenhuizen and L.L.M. Van
	Deenan},
  title = {Purification and properties of an anionic zymogen of phospholipase
	{A} from porcine pancreas},
  journal = BBA,
  year = {1968},
  volume = {159},
  pages = {103--117},
  annote = {PC bilayer: poor substrate}
}

@ARTICLE{JENS68,
  author = {E.~V.~Jensen and T.~Suzuki and T.~Kawashima and W.~E.~Stumpf and
	P.~W.~Jungblut and E.~R.~DeSombre},
  title = {A two-step mechanism for the interaction of estradiol with rat uterus},
  journal = PNAS,
  year = {1968},
  volume = {59},
  pages = {632--638}
}

@ARTICLE{PAPA68,
  author = {D. Papahadjopoulos},
  title = {Surface properties of acidic phospholipids: interaction of monolayers
	and hydrated liquid crystals with uni- and bi- valent metal ions},
  journal = BBA,
  year = {1968},
  volume = {163},
  pages = {240--254}
}

@ARTICLE{Stra68,
  author = {G. Strang},
  title = {On the construction and comparison of difference schemes},
  journal = SJNA,
  year = {1968},
  volume = {5},
  pages = {506--517},
  nremark = {cited in SaCa94 p.~163}
}

@ARTICLE{WALD68,
  author = {George Wald},
  title = {The Molecular Basis of Visual Excitation},
  journal = NAT,
  year = {1968},
  volume = {219},
  pages = {800--807}
}

@INPROCEEDINGS{AMDA67,
  author = {G. M. Amdahl},
  title = {Validity of the Single Processor Approach to Achieve Large Scale
	Computing Capabilities},
  booktitle = {Proc. AFIPS Spring Computer Conf.},
  year = {1967},
  volume = {30},
  pages = {483--485},
  address = {Reston, Va},
  publisher = {AFIPS Press},
  annote = {ref for famous Amdahl's law}
}

@ARTICLE{Bune67,
  author = {O. Buneman},
  title = {Time-Reversible Difference Procedures},
  journal = {J. Comput. Phys.},
  year = {1967},
  volume = {1},
  pages = {517--535}
}

@ARTICLE{Hayl67,
  author = {A. Hayli},
  title = {Le probl\`eme des {N} corps dans un champ ext\'erieur application
	a l'\'evolution dynamique des amas ouverts-{I}},
  journal = {Bulletin Astronomique},
  year = {1967},
  volume = {2},
  pages = {67--89}
}

@BOOK{SUZU67,
  title = {Electronic Absorption Spectra and Geometry of Organic Molecules},
  publisher = {Academic Press},
  year = {1967},
  author = {Hiroshi Leach},
  address = {New York}
}

@ARTICLE{LePV67,
  author = {J.L.~Lebowitz and J.K.~Percus and L.~Verlet},
  title = {Computation of Heat Capacities from Temperature Fluctuations},
  journal = {Phys. Rev.},
  year = {1967},
  volume = {153},
  pages = {250--254}
}

@ARTICLE{SMAL67,
  author = {D. M. Small},
  title = {Phase equilibria and structure of dry and hydrated egg lecithin},
  journal = JLR,
  year = {1967},
  volume = {8},
  pages = {551--557},
  annote = {requested Tx=19920908.}
}

@ARTICLE{Verl67,
  author = {L. Verlet},
  title = {Computer `Experiments' on Condensed Fluids \mbox{I}. {T}hermodynamical
	Properties of \mbox{Lennard--Jones} Molecules},
  journal = {Phys. Rev.},
  year = {1967},
  volume = {159},
  pages = {98--103}
}

@ARTICLE{Bakh66,
  author = {N.~S. Bakhvalov},
  title = {On the convergence of a relaxation method with natural constraints
	on the elliptic operator},
  journal = {USSR Comput. Math. Phys.},
  year = {1966},
  volume = {6},
  number = {101--135}
}

@ARTICLE{BANG66,
  author = {A. D. Bangham and D. Papahadjopoulos},
  title = {Biophysical properties of phospholipids. I. Interaction of phosphotidylserine
	monolayers with metal ions.},
  journal = BBA,
  year = {1966},
  volume = {126},
  pages = {181--184}
}

@BOOK{COTT66,
  title = {Advanced Inorganic Chemistry},
  publisher = {Interscience Publishers},
  year = {1966},
  author = {F.A. Cotton and G. Wilkinson},
  address = {New York}
}

@BOOK{SALE66,
  title = {The Molecular Orbital Theory of Conjugated Systems},
  publisher = {W. A. Benjamin},
  year = {1966},
  author = {L. Salem},
  address = {New York, Amsterdam}
}

@ARTICLE{SAUE66,
  author = {K. Sauer and J. R. Lindsay Smith and A. J. Schultz},
  title = {The dimerization of Chlorophyll a, Chlorophyll b and Bacteriochlorophyll
	in solution},
  journal = JACS,
  year = {1966},
  volume = {88},
  pages = {2681--2688}
}

@BOOK{Wadd66,
  title = {Principles of Development and Differentiation},
  publisher = {Macmillan Company},
  year = {1966},
  author = {C.H. Waddington},
  address = {New York}
}

@ARTICLE{WILT66,
  author = {W. Wiltschko and F.W. Merkel},
  title = {Orientierung zugunruhiger {R}otkehlchen im statischen {M}agnetfeld},
  journal = {Verh.\ dt.\ zool.\ Ges.},
  year = {1966},
  volume = {59},
  pages = {362--367}
}

@BOOK{AbSt65,
  title = {Handbook of Mathematical Functions},
  publisher = {Dover},
  year = {1965},
  author = {M.~Abramowitz and I.~A.~Stegun},
  address = {New York}
}

@INBOOK{FOER65,
  pages = {93--137},
  title = {Delocalized Excitation and Excitation Transfer},
  publisher = {Academic Press},
  year = {1965},
  editor = {O. Sinanoglu},
  author = {T. F{\"o}rster},
  address = {New York},
  booktitle = {Modern Quantum Chemistry. Part {III}: Action of light and organic
	crystals}
}

@BOOK{Gold65,
  title = {Classical Mechanics},
  publisher = {Addison-Wesley},
  year = {1965},
  author = {H. Goldstein}
}

@ARTICLE{MORI65,
  author = {Mori, H.},
  title = {Transport, Collective Motion, and Brownian Motion},
  journal = {Theoret. Phys.},
  year = {1965},
  volume = {33},
  pages = {423}
}

@BOOK{Dira64,
  title = {Lectures on Quantum Mechanics},
  publisher = {Yeshiva University},
  year = {1964},
  author = {Dirac, P.A.M.},
  series = {Belfer Graduate School Monographs, No. 3}
}

@ARTICLE{HeHe64,
  author = {M. H{\'e}non and C. Heiles},
  title = {The Applicability of the Third Integral of Motion: Some Numerical
	Experiments},
  journal = {Astron. J.},
  year = {1964},
  volume = {69},
  pages = {73--79},
  number = {1}
}

@BOOK{KeKu64,
  title = {BASIC Instruction Manual},
  publisher = {Dartmouth College},
  year = {1964},
  author = {J. G. Kemeny and T. E. Kurtz},
  address = {Hanover, NH}
}

@ARTICLE{Rahm64,
  author = {A. Rahman},
  title = {Correlation in the Motion of Atoms in Liquid Argon},
  journal = {Phys. Rev. A},
  year = {1964},
  volume = {136},
  pages = {405--411}
}

@ARTICLE{HOOG63,
  author = {K.~Hoogsteen},
  title = {The crystal and molecular structure of a hydrogen--bonded complex
	between 1-methyl thymin and 9-methyl adenine},
  journal = AC,
  year = {1963},
  volume = {16},
  pages = {907--916},
  annote = {the paper that defines what hoogsteen hydrogen bonds are}
}

@ARTICLE{RaRS63,
  author = {G. N. Ramachandran and C. Ramakrishnan and V. Sasisekharan},
  title = {Stereochemistry of Polypeptide Chain Configurations},
  journal = JMB,
  year = {1963},
  volume = {7},
  pages = {95--99}
}

@ARTICLE{STEI63,
  author = {M. S. Steinberg},
  title = {Reconstruction of tissues by dissociated cells},
  journal = SCI,
  year = {1963},
  volume = {141},
  pages = {401--408},
  number = {3579}
}

@BOOK{DAVY62,
  title = {Theory of Molecular Excitons},
  publisher = {McGraw-Hill},
  year = {1962},
  author = {A. S. Davydov},
  address = {New York}
}

@ARTICLE{HUBE62,
  author = {D.~Hubel and T.~N. Wiesel},
  title = {Receptive fields, binocular interaction and functional architecture
	in the cat's striate cortex},
  journal = {J. Physiol. (Lond.)},
  year = {1962},
  volume = {160},
  pages = {106--154}
}

@ARTICLE{LUZZ62,
  author = {V. Luzzati and F. Husson},
  title = {The structure of the liquid-crystalline phases of lipid-water systems},
  journal = JCB,
  year = {1962},
  volume = {12},
  pages = {201--219},
  annote = {requested Tx=19920908.}
}

@ARTICLE{Mose62,
  author = {J. Moser},
  title = {On Invariant Curves of Area-Preserving Mappings of an Annulus},
  journal = {Nachr.\ Akad.\ Wiss.\ G\"ottingen II Math.-Phys.\ Kl.},
  year = {1962},
  pages = {1--20},
  nremark = {MR 26 #5255; 506 GEMN6 MTX}
}

@ARTICLE{ROSS62,
  author = {Rossmann, M. G. and Blow, D. M.},
  title = {The Detection of Sub-Units within the Crystallographic Asymmetric
	Unit},
  journal = {Acta Cryst.},
  year = {1962},
  volume = {A15},
  pages = {24--31}
}

@ARTICLE{Fedo61,
  author = {R.~P. Fedorenko},
  title = {A relaxation method for solving elliptic differential equations},
  journal = {USSR Comput. Math. Phys.},
  year = {1961},
  volume = {1},
  pages = {1092}
}

@ARTICLE{GOUT61,
  author = {M. Gouterman},
  title = {Spectra of porphyrins},
  journal = {J. Mol. Spectrosc.},
  year = {1961},
  volume = {6},
  pages = {138--163}
}

@ARTICLE{JACO61,
  author = {F.~Jacob and J.~Monod},
  title = {Genetic Regulatory Mechanisms in the Synthesis of Proteins},
  journal = JMB,
  year = {1961},
  volume = {3},
  pages = {318--356},
  annote = {one of the early papers}
}

@ARTICLE{ZWAN61,
  author = {R. Zwanzig},
  title = {Memory Effects in Irreversible Thermodynamics},
  journal = PR,
  year = {1961},
  volume = {124},
  pages = {983}
}

@ARTICLE{ALDE60,
  author = {B. J. Alder and T. E. Wainwright},
  title = {Studies in Molecular Dynamics {II}. Behavior of a Small Number of
	Elastic Spheres},
  journal = JCP,
  year = {1960},
  volume = {33},
  pages = {1439--1451}
}

@ARTICLE{GLAR60,
  author = {S. H. Glarum},
  title = {Dielectric relaxation of polar liquids},
  journal = JCP,
  year = {1960},
  volume = {33},
  pages = {1371}
}

@ARTICLE{Good60,
  author = {L. A. Goodman},
  title = {On the exact variance of products},
  journal = JASA,
  year = {1960},
  volume = {55},
  pages = {708--713}
}

@BOOK{MBE+60,
  title = {Lisp 1 Programmer's Manual},
  publisher = {Artificial Intelligence Group, Computation Center and Research Laboratory
	of Electronics, MIT},
  year = {1960},
  author = {J. McCarthy and R. Brayton and D. Edwards and P. Fox and L. Hodes
	and D. Luckham and K. Maling and D. Park and S. Russell},
  address = {Cambridge, MA}
}

@BOOK{PiMc60,
  title = {The Hydrogen Bond},
  publisher = {W. H. Freeman and Co.},
  year = {1960},
  editor = {Linus Pauling},
  author = {George C. Pimentel and Aubrey L. McClellan},
  address = {San Francisco and London}
}

@ARTICLE{RICE60,
  author = {Stuart A. Rice},
  title = {Some Further Remarks on the Coefficient of Self Diffusion in Simple
	Dense Fluids},
  journal = JCP,
  year = {1960},
  volume = {33},
  pages = {1376--1378}
}

@BOOK{WHIT60,
  title = {A treatise on the analytical dynamics of particles and rigid bodies,
	with an introduction to the problem of three bodies},
  publisher = {Cambridge University Press},
  year = {1960},
  author = {E. T. Whittaker},
  address = {Cambridge, UK},
  edition = {4}
}

@ARTICLE{COHE59,
  author = {M. H. Cohen and D. Turnbull},
  title = {Molecular transport in liquids and gasses},
  journal = JCP,
  year = {1959},
  volume = {31},
  pages = {1164},
  annote = {requested Tx=19921102.}
}

@ARTICLE{MiRe59,
  author = {W. E. Milne and R. R. Reynolds},
  title = {Stability of a Numerical Solution of Differential Equations},
  journal = JACM,
  year = {1959},
  volume = {6},
  pages = {196--203},
  number = {2}
}

@ARTICLE{Newm59,
  author = {N. M. Newmark},
  title = {A Method of Computation for Structural Dynamics},
  journal = {ASCE J. Engrg.\ Mech.\ Division},
  year = {1959},
  volume = {85},
  pages = {67--94}
}

@ARTICLE{KLOT58,
  author = {I. M. Klotz},
  title = {Protein Hydration and Behavior},
  journal = SCI,
  year = {1958},
  volume = {128},
  pages = {815--822}
}

@ARTICLE{MITC58,
  author = {Peter Mitchell and Jennifer Moyle},
  title = {Enzyme Catalysis and Group Translocation},
  journal = {Proc.\ Roy.\ Phys.\ Soc.\ Edinburgh},
  year = {1958},
  volume = {27},
  pages = {61--72}
}

@ARTICLE{NEPO58,
  author = {B.S. Neporent},
  title = {General relation between absorption and emission for the modulation
	spectra of polyatomic molecules},
  journal = {Sov.~Phys.~Dokl.},
  year = {1958},
  volume = {3},
  pages = {337--340}
}

@BOOK{AiBr57,
  title = {The log-normal distribution},
  publisher = {University Press},
  year = {1957},
  author = {J. Aitchison and J.~A.~C. Brown},
  address = {Cambridge}
}

@ARTICLE{HOPP57,
  author = {Hoppe, W.},
  title = {{Eine neue Methode zur Bestimmung der Kristallstruktur bei ganz oder
	teilweise bekannter Molek\"ulstruktur}},
  journal = {Acta Cryst.},
  year = {1957},
  volume = {10},
  pages = {750--751}
}

@ARTICLE{MUEL57,
  author = {G.C.~Mueller and A.M.~Herranen and K.F.~Jervell},
  title = {Studies on the mechanism of action of estrogens},
  journal = {Recent Prog. Horm. Res.},
  year = {1957},
  volume = {14},
  pages = {95--139}
}

@ARTICLE{RuUn57,
  author = {H. Rubin and P. Ungar},
  title = {Motion Under a Strong Constraining Force},
  journal = {Comm.\ Pure and Appl.\ Math.},
  year = {1957},
  volume = {10},
  pages = {65--87}
}

@ARTICLE{STEP57,
  author = {B.I. Stepanov},
  title = {A universal relation between absorption and luminescence spectra
	of complex molecules},
  journal = {Sov.~Phys.~Dokl.},
  year = {1957},
  volume = {2},
  pages = {81--84}
}

@ARTICLE{TANF57,
  author = {C.\ Tanford and J.\ G.\ Kirkwood},
  title = {Theory of Protein Titration Curves},
  journal = JACS,
  year = {1957},
  volume = {79},
  pages = {5333--5352}
}

@TECHREPORT{Devo56,
  author = {R.~{De Vogela{\'e}re}},
  title = {Methods of Integration Which Preserve the Contact Transformation
	Property of {H}amiltonian Equations},
  institution = {Department of Mathematics, University of Notre Dame},
  year = {1956},
  number = {4}
}

@ARTICLE{MARC56A,
  author = {R. A. Marcus},
  title = {On the Energy of Oxidation-Reduction Reactions Involving Electron
	Transfer.\ {I}},
  journal = JCP,
  year = {1956},
  volume = {24},
  pages = {966--978}
}

@ARTICLE{MARC56B,
  author = {R. A. Marcus},
  title = {Electrostatic Free Energy and Other Properties of States Having Nonequilibrium
	Polarization.\ {II}},
  journal = JCP,
  year = {1956},
  volume = {24},
  pages = {979--989}
}

@ARTICLE{PARI56,
  author = {R. Pariser},
  title = {Theory of the Electronic Spectra and Structure of the Polyacenes
	and of Alternant Hydrocarbons},
  journal = JCP,
  year = {1956},
  volume = {24},
  pages = {250--268}
}

@ARTICLE{TORR56,
  author = {H. C. Torrey},
  title = {Bloch Equations with Diffusion Terms},
  journal = {Phys.~Rev.},
  year = {1956},
  volume = {{\bf 104}},
  pages = {563},
  brief = {This is the original development of the `Torrey' term which is e^(-(1/3)
	D t^3 G^2). Fairly straightforward.}
}

@ARTICLE{KUBO55,
  author = {R. Kubo and Y. Toyozawa},
  title = {Application of the Method of Generating Function to Radiative and
	Non-Radiative Transitions of a Trapped Electron in a Crystal},
  journal = PTP,
  year = {1955},
  volume = {13},
  pages = {160--182}
}

@ARTICLE{SOLO55,
  author = {Solomon, I.},
  title = {Relaxation Processes in a System of 2 Spins},
  journal = PR,
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@Article{Morc10c,
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